Commands
Planemo is a set of utilities for developing Galaxy tools. Each utility is
implemented as a subcommand of the planemo
executable. This section of the
documentation describes these commands.
autoupdate
command
This section is auto-generated from the help text for the planemo command
autoupdate
. This help message can be generated with planemo autoupdate
--help
.
Usage:
planemo autoupdate [OPTIONS] TOOL_PATH
Help
Auto-update tool requirements by checking against Conda and updating if newer versions are available. Options:
--dry-run Perform a dry run autoupdate without modifying
the XML files.
-r, --recursive Recursively perform command for
subdirectories.
--test Test updated XML files.
--skiplist TEXT Skiplist file, containing a list of tools or
workflows for which autoupdate should be
skipped.
--skip_requirements TEXT Comma-separated list of requirements which
should be not be updated. Default is
python,r-base,perl.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--paste_test_data_paths / --no_paste_test_data_paths
By default Planemo will use or not use
Galaxy's path paste option to load test data
into a history based on the engine type it is
targeting. This can override the logic to
explicitly enable or disable path pasting.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--report_level [all|warn|error]
--report_xunit PATH Output an XUnit report, useful for CI testing
--fail_level [warn|error]
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
--help Show this message and exit.
ci_find_repos
command
This section is auto-generated from the help text for the planemo command
ci_find_repos
. This help message can be generated with planemo ci_find_repos
--help
.
Usage:
planemo ci_find_repos [OPTIONS] PROJECT
Help
Find all shed repositories in one or more directories.
Currently, a repository is considered any directory with a .shed.yml or .dockstore.yml file.
Options:
--exclude PATH Paths to exclude.
--exclude_from FILE File of paths to exclude.
--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
--chunk_count INTEGER Split output into chunks of this many item and
print --chunk such group.
--chunk INTEGER When output is split into --chunk_count
groups, output the group 0-indexedby this
option.
--output TEXT File to output to, or - for standard output.
--help Show this message and exit.
ci_find_tools
command
This section is auto-generated from the help text for the planemo command
ci_find_tools
. This help message can be generated with planemo ci_find_tools
--help
.
Usage:
planemo ci_find_tools [OPTIONS] PROJECT
Help
Find all tools in one or more directories.
Tools can be chunked up, filtered, etc… to build lists of tools to perform operations over for continuous integration operations.
Options:
--exclude PATH Paths to exclude.
--exclude_from FILE File of paths to exclude.
--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
--chunk_count INTEGER Split output into chunks of this many item and
print --chunk such group.
--chunk INTEGER When output is split into --chunk_count
groups, output the group 0-indexedby this
option.
--output TEXT File to output to, or - for standard output.
--group_tools Group tools of the same repository on a single
line.
--help Show this message and exit.
ci_setup
command
This section is auto-generated from the help text for the planemo command
ci_setup
. This help message can be generated with planemo ci_setup
--help
.
Usage:
planemo ci_setup [OPTIONS]
Help
Launch Galaxy instance, then terminate instance.
Useful for populating a CI cache.
Options:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--help Show this message and exit.
clone
command
This section is auto-generated from the help text for the planemo command
clone
. This help message can be generated with planemo clone
--help
.
Usage:
planemo clone [OPTIONS] TARGET PROJECT
Help
Short-cut to quickly clone, fork, and branch a relevant Github repo.
For instance, the following will clone, fork, and branch the tools-iuc repository to allow a subsequent pull request to fix a problem with bwa.
$ planemo clone --branch bwa-fix tools-iuc
$ cd tools-iuc
$ # Make changes.
$ git add -p # Add desired changes.
$ git commit -m "Fix bwa problem."
$ planemo pull_request -m "Fix bwa problem."
These changes do require that a github access token is specified in ~/.planemo.yml. An access token can be generated by going to https://github.com/settings/tokens.
Options:
--fork / --skip_fork
--branch TEXT Create a named branch on result.
--help Show this message and exit.
conda_build
command
This section is auto-generated from the help text for the planemo command
conda_build
. This help message can be generated with planemo conda_build
--help
.
Usage:
planemo conda_build [OPTIONS] RECIPE_DIR
Help
Perform conda build with Planemo’s conda. Options:
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--help Show this message and exit.
conda_env
command
This section is auto-generated from the help text for the planemo command
conda_env
. This help message can be generated with planemo conda_env
--help
.
Usage:
planemo conda_env [OPTIONS] TOOL_PATH
Help
Activate a conda environment for tool.
Source the output of this command to activate a conda environment for this tool.
$ . <(planemo conda_env seqtk_seq.xml)
Deactivate environment with conda_env_deactivate
(seqtk_seq_v6) $ which seqtk
/home/planemo/miniconda2/envs/jobdepsDkzcjjfecc6d406196737781ff4456ec60975c137e04884e4f4b05dc68192f7cec4656/bin/seqtk
(seqtk_seq_v6) $ conda_env_deactivate
$
Options:
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--help Show this message and exit.
conda_init
command
This section is auto-generated from the help text for the planemo command
conda_init
. This help message can be generated with planemo conda_init
--help
.
Usage:
planemo conda_init [OPTIONS]
Help
Download and install conda.
This will download conda for managing dependencies for your platform using the appropriate Miniconda installer.
By running this command, you are agreeing to the terms of the conda license a 3-clause BSD 3 license. Please review full license at http://docs.continuum.io/anaconda/eula.
Planemo will print a warning and terminate with an exit code of 7 if Conda is already installed.
Options:
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--help Show this message and exit.
conda_install
command
This section is auto-generated from the help text for the planemo command
conda_install
. This help message can be generated with planemo conda_install
--help
.
Usage:
planemo conda_install [OPTIONS] TARGET
Help
Install conda packages for tool requirements. Options:
-r, --recursive Recursively perform command for
subdirectories.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--global Install Conda dependencies globally instead of
in requirement specific environments packaged
for tools. If the Conda bin directory is on
your PATH, tools may still use binaries but
this is more designed for interactive testing
and debugging.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--help Show this message and exit.
conda_search
command
This section is auto-generated from the help text for the planemo command
conda_search
. This help message can be generated with planemo conda_search
--help
.
Usage:
planemo conda_search [OPTIONS] TERM
Help
Perform conda search with Planemo’s conda.
Implicitly adds channels Planemo is configured with.
Options:
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--help Show this message and exit.
config_init
command
This section is auto-generated from the help text for the planemo command
config_init
. This help message can be generated with planemo config_init
--help
.
Usage:
planemo config_init [OPTIONS] PROJECT
Help
Initialise global configuration for Planemo.
Helps initialize global configuration (in home directory) for Planemo.
Options:
--template TEXT
--help Show this message and exit.
container_register
command
This section is auto-generated from the help text for the planemo command
container_register
. This help message can be generated with planemo container_register
--help
.
Usage:
planemo container_register [OPTIONS] TOOL_PATH
Help
Register multi-requirement containers as needed.
BioContainers publishes all Bioconda packages automatically as individual container images. These however are not enough for tools with multiple best-practice requirements. Such requirements should be recorded and published so that a container can be created and registered for these tools.
Options:
-r, --recursive Recursively perform command for
subdirectories.
--mulled_namespace TEXT Build a mulled image with the specified
namespace - defaults to biocontainers. Galaxy
currently only recognizes images with the
namespace biocontainers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--output_directory DIRECTORY Container registration directory (defaults to
~/.planemo/multi-package-containers.
-m, --message TEXT Commit and pull request message template for
registration interactions.
--pull_request / --no_pull_request
Fork and create a pull request against
BioContainers/multi-package-containers for
these changes.
--force_push / --no_force_push Force push branch for pull request in case it
already exists.
--help Show this message and exit.
create_alias
command
This section is auto-generated from the help text for the planemo command
create_alias
. This help message can be generated with planemo create_alias
--help
.
Usage:
planemo create_alias [OPTIONS] OBJ
Help
Add an alias for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.
Options:
--alias TEXT Name of an alias.
--profile TEXT Name of profile (created with the profile_create command) to
use with this command. [required]
--help Show this message and exit.
database_create
command
This section is auto-generated from the help text for the planemo command
database_create
. This help message can be generated with planemo database_create
--help
.
Usage:
planemo database_create [OPTIONS] IDENTIFIER
Help
Create a development database.
Currently the only implementation is postgres which will be managed with
psql
.
Planemo database_
commands make it very easy to create and destroy
databases, therefore it should not be used for production data - and it
should not even be connnected to a production database server. Planemo
is intended for development purposes only.
Planemo will assume that it can manage and access postgres databases
without specifying a password. This can be accomplished by configuring
postgres to not required a password for the planemo user or by specifying
a password in a .pgpass
file.
Planemo can be configured to not require a password for the planemo user in
the postgres configuration file pg_hba.conf
(on Ubuntu/Debian linux
distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
Adding the following lines to that file will allow planemo and Galaxy to
access the databases without a password.
# "local" is for Unix domain socket connections only
local all all trust
# IPv4 local connections:
host all all 127.0.0.1/32 trust
# IPv6 local connections:
host all all ::1/128 trust
More information on the pg_hda.conf
configuration file can be found at
http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
Information on .pgpass
files can be found at at the following location:
http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
Debian distros - a postgres user likely already exists and its password can
be set by setting up a file ~/.pgpass
file with the following contents.
*:*:*:postgres:<postgres_password>
Options:
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--help Show this message and exit.
database_delete
command
This section is auto-generated from the help text for the planemo command
database_delete
. This help message can be generated with planemo database_delete
--help
.
Usage:
planemo database_delete [OPTIONS] IDENTIFIER
Help
Delete a development database.
Currently the only implementation is postgres which will be managed with
psql
.
Planemo database_
commands make it very easy to create and destroy
databases, therefore it should not be used for production data - and it
should not even be connnected to a production database server. Planemo
is intended for development purposes only.
Planemo will assume that it can manage and access postgres databases
without specifying a password. This can be accomplished by configuring
postgres to not required a password for the planemo user or by specifying
a password in a .pgpass
file.
Planemo can be configured to not require a password for the planemo user in
the postgres configuration file pg_hba.conf
(on Ubuntu/Debian linux
distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
Adding the following lines to that file will allow planemo and Galaxy to
access the databases without a password.
# "local" is for Unix domain socket connections only
local all all trust
# IPv4 local connections:
host all all 127.0.0.1/32 trust
# IPv6 local connections:
host all all ::1/128 trust
More information on the pg_hda.conf
configuration file can be found at
http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
Information on .pgpass
files can be found at at the following location:
http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
Debian distros - a postgres user likely already exists and its password can
be set by setting up a file ~/.pgpass
file with the following contents.
*:*:*:postgres:<postgres_password>
Options:
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--help Show this message and exit.
database_list
command
This section is auto-generated from the help text for the planemo command
database_list
. This help message can be generated with planemo database_list
--help
.
Usage:
planemo database_list [OPTIONS]
Help
List databases in configured database source.
Currently the only implementation is postgres which will be managed with
psql
.
Planemo database_
commands make it very easy to create and destroy
databases, therefore it should not be used for production data - and it
should not even be connnected to a production database server. Planemo
is intended for development purposes only.
Planemo will assume that it can manage and access postgres databases
without specifying a password. This can be accomplished by configuring
postgres to not required a password for the planemo user or by specifying
a password in a .pgpass
file.
Planemo can be configured to not require a password for the planemo user in
the postgres configuration file pg_hba.conf
(on Ubuntu/Debian linux
distros this file is in /etc/postgresql/<postgres_version>/main/ directory).
Adding the following lines to that file will allow planemo and Galaxy to
access the databases without a password.
# "local" is for Unix domain socket connections only
local all all trust
# IPv4 local connections:
host all all 127.0.0.1/32 trust
# IPv6 local connections:
host all all ::1/128 trust
More information on the pg_hda.conf
configuration file can be found at
http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html.
Information on .pgpass
files can be found at at the following location:
http://www.postgresql.org/docs/9.4/static/libpq-pgpass.html. In Ubuntu and
Debian distros - a postgres user likely already exists and its password can
be set by setting up a file ~/.pgpass
file with the following contents.
*:*:*:postgres:<postgres_password>
Options:
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--help Show this message and exit.
delete_alias
command
This section is auto-generated from the help text for the planemo command
delete_alias
. This help message can be generated with planemo delete_alias
--help
.
Usage:
planemo delete_alias [OPTIONS]
Help
List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.
Options:
--alias TEXT Name of an alias. [required]
--profile TEXT Name of profile (created with the profile_create command) to
use with this command. [required]
--help Show this message and exit.
docker_build
command
This section is auto-generated from the help text for the planemo command
docker_build
. This help message can be generated with planemo docker_build
--help
.
Usage:
planemo docker_build [OPTIONS] TOOL_PATH
Help
Build (and optionally cache) Docker images.
Loads the tool or tools referenced by TOOL_PATH
(by default all tools
in current directory), and ensures they all reference the same Docker image
and then attempts to find a Dockerfile for these tools (can be explicitly
specified with --dockerfile
but by default it will check the tool’s
directory and the current directory as well).
This command will then build and tag the image so it is ready to be tested and published. The docker_shell command be used to test out the built image.
% planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
% planemo docker_shell --from_tag bowtie2.xml
This can optionally also cache the images.
Options:
--dockerfile TEXT
--docker_image_cache TEXT
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--help Show this message and exit.
docker_shell
command
This section is auto-generated from the help text for the planemo command
docker_shell
. This help message can be generated with planemo docker_shell
--help
.
Usage:
planemo docker_shell [OPTIONS] TOOL_PATH
Help
Launch shell in Docker container for a tool.
Will launch a shell in the Docker container referenced by the specified tool. Prints a command to do this the way Galaxy would in job files it generates - so be sure to wrap this in $(…) to launch the subshell.
$ $(planemo docker_shell bowtie2.xml)
...
root@b8754062f875:/#
Options:
--from_tag Treat the tool's Docker container identifier
as a locally cached tag.
--shell TEXT Shell to launch in container (defaults to
/bin/bash).
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--help Show this message and exit.
dockstore_init
command
This section is auto-generated from the help text for the planemo command
dockstore_init
. This help message can be generated with planemo dockstore_init
--help
.
Usage:
planemo dockstore_init [OPTIONS] PROJECT
Help
Initialize a .dockstore.yml configuration file for workflows in directory.
Walk supplied directory and find all Galaxy workflows and test configurations
and create a .dockstore.yml
with references to these files. Be sure to push
this file to Github before registering your workflow repository with Dockstore.
Visit Dockstore at https://dockstore.org/. Find more about registering workflows with Dockstore at https://docs.dockstore.org/en/develop/getting-started/dockstore-workflows.html.
Options:
--publish / --no_publish Set publish attribute to true in .dockstore.yml file
--help Show this message and exit.
docs
command
This section is auto-generated from the help text for the planemo command
docs
. This help message can be generated with planemo docs
--help
.
Usage:
planemo docs [OPTIONS]
Help
Open Planemo documentation in web browser. Options:
--help Show this message and exit.
lint
command
This section is auto-generated from the help text for the planemo command
lint
. This help message can be generated with planemo lint
--help
.
Usage:
planemo lint [OPTIONS] TOOL_PATH
Help
Check for common errors and best practices. Options:
--report_level [all|warn|error]
--report_xunit PATH Output an XUnit report, useful for CI testing
--fail_level [warn|error]
-s, --skip TEXT Comma-separated list of lint tests to skip
(e.g. passing --skip 'citations,xml_order'
would skip linting of citations and best-
practice XML ordering.
--skip_file FILE File containing a list of lint tests to skip
-r, --recursive Recursively perform command for
subdirectories.
--urls Check validity of URLs in XML files
--doi Check validity of DOIs in XML files
--conda_requirements Check tool requirements for availability in
best practice Conda channels.
--biocontainer, --biocontainers
Check best practice BioContainer namespaces
for a container definition applicable for this
tool.
--help Show this message and exit.
list_alias
command
This section is auto-generated from the help text for the planemo command
list_alias
. This help message can be generated with planemo list_alias
--help
.
Usage:
planemo list_alias [OPTIONS]
Help
List aliases for a path or a workflow or dataset ID. Aliases are associated with a particular planemo profile.
Options:
--profile TEXT Name of profile (created with the profile_create command) to
use with this command. [required]
--help Show this message and exit.
list_invocations
command
This section is auto-generated from the help text for the planemo command
list_invocations
. This help message can be generated with planemo list_invocations
--help
.
Usage:
planemo list_invocations [OPTIONS] WORKFLOW_IDENTIFIER
Help
Get a list of invocations for a particular workflow ID or alias.
Options:
--profile TEXT Name of profile (created with the profile_create command) to
use with this command. [required]
--help Show this message and exit.
list_repos
command
This section is auto-generated from the help text for the planemo command
list_repos
. This help message can be generated with planemo list_repos
--help
.
Usage:
planemo list_repos [OPTIONS] PROJECT
Help
Find all shed repositories in one or more directories and output as yaml.
Currently, a shed repository is considered a directory with a .shed.yml file.
Options:
--exclude PATH Paths to exclude.
--exclude_from FILE File of paths to exclude.
--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
--chunk_count INTEGER Split output into chunks of this many item and
print --chunk such group.
--chunk INTEGER When output is split into --chunk_count
groups, output the group 0-indexedby this
option.
--output TEXT File to output to, or - for standard output.
--help Show this message and exit.
merge_test_reports
command
This section is auto-generated from the help text for the planemo command
merge_test_reports
. This help message can be generated with planemo merge_test_reports
--help
.
Usage:
planemo merge_test_reports [OPTIONS] INPUT_PATHS FILE_PATH
Help
Merge tool_test_output.json files from multiple runs. Options:
--help Show this message and exit.
mull
command
This section is auto-generated from the help text for the planemo command
mull
. This help message can be generated with planemo mull
--help
.
Usage:
planemo mull [OPTIONS] TOOL_PATH
Help
Build containers for specified tools.
Supplied tools will be inspected for referenced requirement packages. For each combination of requirements a “mulled” container will be built. Galaxy can automatically discover this container and subsequently use it to run or test the tool.
For this to work, the tool’s requirements will need to be present in a known
Conda channel such as bioconda (https://github.com/bioconda/bioconda-recipes).
This can be verified by running planemo lint --conda_requirements
on the
target tool(s).
Options:
-r, --recursive Recursively perform command for
subdirectories.
--mulled_conda_version TEXT Install a specific version of Conda before
running the command, by default the version
that comes with the continuumio miniconda3
image will be used under Linux and under Mac
OS X Conda will be upgraded to to work around
a bug in 4.2.
--mulled_namespace TEXT Build a mulled image with the specified
namespace - defaults to biocontainers. Galaxy
currently only recognizes images with the
namespace biocontainers.
--mulled_command TEXT Mulled action to perform for targets - this
defaults to 'build-and-test'.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--help Show this message and exit.
mulled_init
command
This section is auto-generated from the help text for the planemo command
mulled_init
. This help message can be generated with planemo mulled_init
--help
.
Usage:
planemo mulled_init [OPTIONS]
Help
Download and install involucro for mull command.
This will happen automatically when using the mull command, but this can be pre-installed in an environment using this command.
Options:
--mulled_conda_version TEXT Install a specific version of Conda before
running the command, by default the version that
comes with the continuumio miniconda3 image will
be used under Linux and under Mac OS X Conda will
be upgraded to to work around a bug in 4.2.
--mulled_namespace TEXT Build a mulled image with the specified namespace
- defaults to biocontainers. Galaxy currently
only recognizes images with the namespace
biocontainers.
--mulled_command TEXT Mulled action to perform for targets - this
defaults to 'build-and-test'.
--help Show this message and exit.
normalize
command
This section is auto-generated from the help text for the planemo command
normalize
. This help message can be generated with planemo normalize
--help
.
Usage:
planemo normalize [OPTIONS] TOOL_PATH
Help
Generate normalized tool XML from input.
This will break the formatting of your tool and is currently only intended for viewing macro expansions for for use with XSD validation (see https://github.com/JeanFred/Galaxy-XSD for instance). Please do not use the output as is - it frequently makes tool less readable not more.
The top-level blocks will be reordered and whitespace fixed according to the tool development best practices outlined on the Galaxy wiki.
% # Print normalized version of tool.
% planemo normalize tool.xml
<tool>
...
% # Print a variant of tool with all macros expanded out, useful for
% # debugging complex macros.
% planemo normalize --expand_macros tool.xml
<tool>
...
Options:
--expand_macros Expand macros while normalizing tool XML - useful to see how
macros are evaluated.
--skip_reorder Planemo will reorder top-level tool blocks according to tool
development best practices as part of this command, this flag
will disable that behavior.
--skip_reindent Planemo will reindent the XML according to tool development
best practices as part of this command, this flag will
disable that behavior.
--help Show this message and exit.
open
command
This section is auto-generated from the help text for the planemo command
open
. This help message can be generated with planemo open
--help
.
Usage:
planemo open [OPTIONS] PATH
Help
Open latest Planemo test results in a web browser. Options:
--help Show this message and exit.
profile_create
command
This section is auto-generated from the help text for the planemo command
profile_create
. This help message can be generated with planemo profile_create
--help
.
Usage:
planemo profile_create [OPTIONS] PROFILE_NAME
Help
Create a profile. Options:
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
--help Show this message and exit.
profile_delete
command
This section is auto-generated from the help text for the planemo command
profile_delete
. This help message can be generated with planemo profile_delete
--help
.
Usage:
planemo profile_delete [OPTIONS] PROFILE_NAME
Help
Delete a profile. Options:
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--help Show this message and exit.
profile_list
command
This section is auto-generated from the help text for the planemo command
profile_list
. This help message can be generated with planemo profile_list
--help
.
Usage:
planemo profile_list [OPTIONS]
Help
List configured profile names. Options:
--help Show this message and exit.
project_init
command
This section is auto-generated from the help text for the planemo command
project_init
. This help message can be generated with planemo project_init
--help
.
Usage:
planemo project_init [OPTIONS] PROJECT
Help
(Experimental) Initialize a new tool project.
This is only a proof-of-concept demo right now.
Options:
--template TEXT
--help Show this message and exit.
pull_request
command
This section is auto-generated from the help text for the planemo command
pull_request
. This help message can be generated with planemo pull_request
--help
.
Usage:
planemo pull_request [OPTIONS] PROJECT
Help
Short-cut to quickly create a pull request for a relevant Github repo.
For instance, the following will clone, fork, and branch the tools-iuc repository to allow a subsequent pull request to fix a problem with bwa.
$ planemo clone --branch bwa-fix tools-iuc
$ cd tools-iuc
$ # Make changes.
$ git add -p # Add desired changes.
$ git commit -m "Fix bwa problem."
$ planemo pull_request -m "Fix bwa problem."
These changes do require that a github access token is specified in ~/.planemo.yml. An access token can be generated by going to https://github.com/settings/tokens.
Options:
-m, --message TEXT Message describing the pull request to create.
--help Show this message and exit.
rerun
command
This section is auto-generated from the help text for the planemo command
rerun
. This help message can be generated with planemo rerun
--help
.
Usage:
planemo rerun [OPTIONS] RERUNNABLE_IDS
Help
Planemo command for rerunning and remapping failed jobs on an external Galaxy server. Supply a list of history, invocation or job IDs, identifying the ID type using the –invocation, –history or –job flag, and all associated failed jobs will be rerun.
Please note: attempting to rerun non-remappable jobs will result in an exit code of 1. As jobs cannot be remapped more than once, running this command two or more times with the same history or job IDs will therefore return an exit code of 1. If avoiding this is important, you should specify the invocation ID instead if possible.
% planemo rerun --invocation / --history / --job RERUNNABLE_IDS
Options:
--profile TEXT Name of profile (created with the profile_create
command) to use with this command.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--invocation Rerun failed jobs associated by one or more invocation
IDs.
--history Rerun failed jobs associated by one or more history
IDs.
--job Rerun failed jobs specified by one or more job IDs.
--help Show this message and exit.
run
command
This section is auto-generated from the help text for the planemo command
run
. This help message can be generated with planemo run
--help
.
Usage:
planemo run [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH
Help
Planemo command for running tools and jobs.
% planemo run cat1-tool.cwl cat-job.json
Options:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--cwl Configure Galaxy for use with CWL tool. (this
option is experimental and will be replaced
when and if CWL support is merged into
Galaxy).
--cwl_galaxy_root DIRECTORY Root of development galaxy directory to
execute command with (must be branch of Galaxy
with CWL support, this option is experimental
and will be replaced with --galaxy_root when
and if CWL support is merged into Galaxy.
--tags TEXT Comma-separated list of tags to add to the
created history.
--output_directory, --outdir DIRECTORY
Where to store outputs of a 'run' task.
--output_json FILE Where to store JSON dictionary describing
outputs of a 'run' task.
--download_outputs / --no_download_outputs
After tool or workflow runs are complete,
download the output files to the location
specified by --output_directory.
--engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
Select an engine to run or test artifacts such
as tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container or the CWL reference implementation
'cwltool' and 'toil' be selected.
--non_strict_cwl Disable strict validation of CWL.
--no-container, --no_container If cwltool engine is used, disable Docker
container usage.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--install_tool_dependencies / --no_install_tool_dependencies
Turn on installation of tool dependencies
using classic toolshed packages.
--install_resolver_dependencies / --no_install_resolver_dependencies
Skip installing tool dependencies through
resolver (e.g. conda).
--install_repository_dependencies / --no_install_repository_dependencies
Skip installing the repository dependencies.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--history_name TEXT Name to give a Galaxy history, if one is
created.
--history_id TEXT Send the results of the run to the history
with the provided ID. A history with this ID
must exist.
--no_wait After invoking a job or workflow, do not wait
for completion.
--paste_test_data_paths / --no_paste_test_data_paths
By default Planemo will use or not use
Galaxy's path paste option to load test data
into a history based on the engine type it is
targeting. This can override the logic to
explicitly enable or disable path pasting.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--help Show this message and exit.
serve
command
This section is auto-generated from the help text for the planemo command
serve
. This help message can be generated with planemo serve
--help
.
Usage:
planemo serve [OPTIONS] TOOL_PATH
Help
Launch Galaxy instance with specified tools.
The Galaxy tool panel will include just the referenced tool or tools (by default all the tools in the current working directory) and the upload tool.
planemo will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the --galaxy_root
option or force planemo to download a disposable instance with the
--install_galaxy
flag.
planemo
will run the Galaxy instance in an existing virtualenv if one
exists in a .venv
directory in the specified --galaxy_root
.
Otherwise, the Galaxy instance will run in a clean virtualenv created in
/tmp
.
planemo
uses temporarily generated config files and environment
variables to attempt to shield this execution of Galaxy from manually
launched runs against that same Galaxy root - but this may not be bullet
proof yet, so please be careful and do not try this against a production
Galaxy instance.
Options:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--cwl Configure Galaxy for use with CWL tool. (this
option is experimental and will be replaced
when and if CWL support is merged into
Galaxy).
--cwl_galaxy_root DIRECTORY Root of development galaxy directory to
execute command with (must be branch of Galaxy
with CWL support, this option is experimental
and will be replaced with --galaxy_root when
and if CWL support is merged into Galaxy.
--help Show this message and exit.
shed_build
command
This section is auto-generated from the help text for the planemo command
shed_build
. This help message can be generated with planemo shed_build
--help
.
Usage:
planemo shed_build [OPTIONS] TOOL_PATH
Help
Create a Galaxy tool tarball.
This will use the .shed.yml file to prepare a tarball (which you could upload to the Tool Shed manually).
Options:
--help Show this message and exit.
shed_create
command
This section is auto-generated from the help text for the planemo command
shed_create
. This help message can be generated with planemo shed_create
--help
.
Usage:
planemo shed_create [OPTIONS] PROJECT
Help
Create a repository in a Galaxy Tool Shed.
This will read the settings from the .shed.yml
file.
Options:
-r, --recursive Recursively perform command for nested repository
directories.
--fail_fast If multiple repositories are specified and an error
occurs stop immediately instead of processing
remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the inferred
tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless shed_key
is specified).
--shed_key TEXT API key for Tool Shed access. An API key is required
unless e-mail and password is specified. This key
can be specified with either --shed_key or
--shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool Shed
access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
-m, --message TEXT Commit message for tool shed upload.
--skip_upload Skip upload contents as part of operation, only
update metadata.
--help Show this message and exit.
shed_diff
command
This section is auto-generated from the help text for the planemo command
shed_diff
. This help message can be generated with planemo shed_diff
--help
.
Usage:
planemo shed_diff [OPTIONS] PROJECT
Help
diff between local repository and Tool Shed.
By default, this will produce a diff between this repository and what would be uploaded to the Tool Shed with the shed_upload command - but this command can be made to compare other combinations of repositories. Here are some examples
$ # diff for this repository and the main Tool Shed
$ planemo shed_diff
$ # diff for this repository and the test Tool Shed
$ planemo shed_diff --shed_target testtoolshed
$ # diff for the test Tool Shed and main Tool Shed
$ planemo shed_diff --shed_target_source testtoolshed
$ # diff for two an explicitly specified repositories (ignores
$ # current project's shed YAML file.)
$ planemo shed_diff --owner peterjc --name blast_rbh
--shed_target_source testtoolshed
This command will return an exit code of:
0 if there are no detected differences.
1 if there are differences.
2 if the target repository doesn’t exist.
>200 if there are errors attempting to perform a diff.
Warning: shed_diff
doesn’t inspect repository metadata, this
difference applies only to the file contents of files that would actually be
uploaded to the repository.
Options:
-r, --recursive Recursively perform command for nested repository
directories.
--fail_fast If multiple repositories are specified and an error
occurs stop immediately instead of processing
remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the inferred
tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless shed_key
is specified).
--shed_key TEXT API key for Tool Shed access. An API key is
required unless e-mail and password is specified.
This key can be specified with either --shed_key or
--shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool Shed
access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
-o, --output PATH Send diff output to specified file.
--shed_target_source TEXT Source Tool Shed to diff against (will ignore local
project info specified). To compare the main Tool
Shed against the test, set this to testtoolshed.
--raw Do not attempt smart diff of XML to filter out
attributes populated by the Tool Shed.
--report_xunit PATH Output an XUnit report, useful for CI testing
--help Show this message and exit.
shed_init
command
This section is auto-generated from the help text for the planemo command
shed_init
. This help message can be generated with planemo shed_init
--help
.
Usage:
planemo shed_init [OPTIONS] PROJECT
Help
Bootstrap new Tool Shed .shed.yml file.
This Tool Shed configuration file is used by other planemo
commands
such as shed_lint
, shed_create
, shed_upload
, and shed_diff
to manage repositories in a Galaxy Tool Shed.
Options:
--from_workflow PATH Attempt to generate repository dependencies
from specified workflow.
--description TEXT Specify repository description for .shed.yml.
--long_description TEXT Specify repository long_description for
.shed.yml.
--remote_repository_url TEXT Specify repository remote_repository_url for
.shed.yml.
--homepage_url TEXT Specify repository homepage_url for .shed.yml.
--category [Assembly|Astronomy|ChIP-seq|Climate Analysis|CLIP-seq|Combinatorial Selections|Computational chemistry|Constructive Solid Geometry|Convert Formats|Data Export|Data Managers|Data Source|Ecology|Entomology|Epigenetics|Fasta Manipulation|Fastq Manipulation|Flow Cytometry Analysis|Genome annotation|Genome editing|Genome-Wide Association Study|Genomic Interval Operations|GIS|Graphics|Imaging|InteractiveTools|Machine Learning|Materials science|Metabolomics|Metagenomics|Micro-array Analysis|Molecular Dynamics|Muon spectroscopy|Nanopore|Next Gen Mappers|NLP|Ontology Manipulation|Phylogenetics|Proteomics|RNA|SAM|Sequence Analysis|Single Cell|Spatial Omics|Statistics|Structural Materials Analysis|Synthetic Biology|Systems Biology|Text Manipulation|Tool Dependency Packages|Tool Generators|Transcriptomics|Variant Analysis|Visualization|Web Services]
Specify repository category for .shed.yml (may
specify multiple).
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the
inferred tool directory name).
-f, --force Overwrite existing files if present.
--help Show this message and exit.
shed_lint
command
This section is auto-generated from the help text for the planemo command
shed_lint
. This help message can be generated with planemo shed_lint
--help
.
Usage:
planemo shed_lint [OPTIONS] PROJECT
Help
Check Tool Shed repository for common issues.
With the --tools
flag, this command lints actual Galaxy tools
in addition to tool shed artifacts.
With the --urls
flag, this command searches for
<package>$URL</package>
and download actions which specify URLs. Each
of those are accessed individually. By default, this tool requests the
first hundred or so bytes of each listed URL and validates that a 200 OK
was received. In tool XML files, the --urls
option checks through the
help text for mentioned URLs and checks those.
Options:
-r, --recursive Recursively perform command for nested
repository directories.
--fail_fast If multiple repositories are specified and an
error occurs stop immediately instead of
processing remaining repositories.
--report_level [all|warn|error]
--fail_level [warn|error]
-s, --skip TEXT Comma-separated list of lint tests to skip
(e.g. passing --skip 'citations,xml_order'
would skip linting of citations and best-
practice XML ordering.
--skip_file FILE File containing a list of lint tests to skip
--tools Lint tools discovered in the process of
linting repositories.
--ensure_metadata Ensure .shed.yml files contain enough metadata
for each repository to allow automated
creation and/or updates.
--urls Check validity of URLs in XML files
--biocontainer, --biocontainers
Check best practice BioContainer namespaces
for a container definition applicable for this
tool.
--help Show this message and exit.
shed_serve
command
This section is auto-generated from the help text for the planemo command
shed_serve
. This help message can be generated with planemo shed_serve
--help
.
Usage:
planemo shed_serve [OPTIONS] PROJECT
Help
Launch Galaxy with Tool Shed dependencies.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and .shed.yml
file(s),
install these artifacts, and serve a Galaxy instances that can be
logged into and explored interactively.
Options:
-r, --recursive Recursively perform command for nested
repository directories.
--fail_fast If multiple repositories are specified and an
error occurs stop immediately instead of
processing remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the
inferred tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless
shed_key is specified).
--shed_key TEXT API key for Tool Shed access. An API key is
required unless e-mail and password is
specified. This key can be specified with
either --shed_key or --shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool
Shed access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--skip_dependencies Do not install shed dependencies as part of
repository installation.
--help Show this message and exit.
shed_test
command
This section is auto-generated from the help text for the planemo command
shed_test
. This help message can be generated with planemo shed_test
--help
.
Usage:
planemo shed_test [OPTIONS] PROJECT
Help
Run tests of published shed artifacts.
This command will start a Galaxy instance configured to target the
specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and .shed.yml
file(s),
install these artifacts, and run the tool tests for these commands.
Options:
-r, --recursive Recursively perform command for nested
repository directories.
--fail_fast If multiple repositories are specified and an
error occurs stop immediately instead of
processing remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the
inferred tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless
shed_key is specified).
--shed_key TEXT API key for Tool Shed access. An API key is
required unless e-mail and password is
specified. This key can be specified with
either --shed_key or --shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool
Shed access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--paste_test_data_paths / --no_paste_test_data_paths
By default Planemo will use or not use
Galaxy's path paste option to load test data
into a history based on the engine type it is
targeting. This can override the logic to
explicitly enable or disable path pasting.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--skip_dependencies Do not install shed dependencies as part of
repository installation.
--help Show this message and exit.
shed_update
command
This section is auto-generated from the help text for the planemo command
shed_update
. This help message can be generated with planemo shed_update
--help
.
Usage:
planemo shed_update [OPTIONS] PROJECT
Help
Update Tool Shed repository.
By default this command will update both repository metadata
from .shed.yml
and upload new contents from the repository
directory.
% planemo shed_update
This will update the main tool shed with the repository defined
by a .shed.yml
file in the current working directory. Both
the location of the .shed.yml
and the tool shed to upload to
can be easily configured. For instance, the following command can
be used if .shed.yml
if contained in path/to/repo
and the
desire is to update the test tool shed.
% planemo shed_update --shed_target testtoolshed path/to/repo
Another important option is --check_diff
- this doesn’t affect the
updating of shed metadata but it will check for differences before
uploading new contents to the tool shed. This may important because the
tool shed will automatically populate certain attributes in tool shed
artifact files (such as tool_dependencies.xml
) and this may
cause unwanted installable revisions to be created when there are no
important changes.
The lower-level shed_upload
command should be used instead if
the repository doesn’t define complete metadata in a .shed.yml
.
Options:
--report_xunit PATH Output an XUnit report, useful for CI testing
-r, --recursive Recursively perform command for nested repository
directories.
--fail_fast If multiple repositories are specified and an
error occurs stop immediately instead of
processing remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the
inferred tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless
shed_key is specified).
--shed_key TEXT API key for Tool Shed access. An API key is
required unless e-mail and password is specified.
This key can be specified with either --shed_key
or --shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool
Shed access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
-m, --message TEXT Commit message for tool shed upload.
--force_repository_creation If a repository cannot be found for the specified
user/repo name pair, then automatically create
the repository in the toolshed.
--check_diff Skip uploading if the shed_diff detects there
would be no 'difference' (only attributes
populated by the shed would be updated.)
--skip_upload Skip upload contents as part of operation, only
update metadata.
--skip_metadata Skip metadata update as part of operation, only
upload new contents.
--help Show this message and exit.
shed_upload
command
This section is auto-generated from the help text for the planemo command
shed_upload
. This help message can be generated with planemo shed_upload
--help
.
Usage:
planemo shed_upload [OPTIONS] PROJECT
Help
Low-level command to upload tarballs.
Generally, shed_update
should be used instead since it also updates
both tool shed contents (via tar ball generation and upload) as well as
metadata (to handle metadata changes in .shed.yml
files).
% planemo shed_upload --tar_only ~/
% tar -tzf shed_upload.tar.gz
test-data/blastdb.loc
...
tools/ncbi_blast_plus/tool_dependencies.xml
% tar -tzf shed_upload.tar.gz | wc -l
117
Options:
-r, --recursive Recursively perform command for nested repository
directories.
--fail_fast If multiple repositories are specified and an
error occurs stop immediately instead of
processing remaining repositories.
--owner TEXT Tool Shed repository owner (username).
--name TEXT Tool Shed repository name (defaults to the
inferred tool directory name).
--shed_email TEXT E-mail for Tool Shed auth (required unless
shed_key is specified).
--shed_key TEXT API key for Tool Shed access. An API key is
required unless e-mail and password is specified.
This key can be specified with either --shed_key
or --shed_key_from_env.
--shed_key_from_env TEXT Environment variable to read API key for Tool
Shed access from.
--shed_password TEXT Password for Tool Shed auth (required unless
shed_key is specified).
-t, --shed_target TEXT Tool Shed to target (this can be 'toolshed',
'testtoolshed', 'local' (alias for
http://localhost:9009/), an arbitrary url or
mappings defined ~/.planemo.yml.
-m, --message TEXT Commit message for tool shed upload.
--force_repository_creation If a repository cannot be found for the specified
user/repo name pair, then automatically create
the repository in the toolshed.
--check_diff Skip uploading if the shed_diff detects there
would be no 'difference' (only attributes
populated by the shed would be updated.)
--tar_only Produce tar file for upload but do not publish to
a tool shed.
--tar FILE Specify a pre-existing tar file instead of
automatically building one as part of this
command.
--help Show this message and exit.
syntax
command
This section is auto-generated from the help text for the planemo command
syntax
. This help message can be generated with planemo syntax
--help
.
Usage:
planemo syntax [OPTIONS]
Help
Open tool config syntax page in web browser. Options:
--help Show this message and exit.
test
command
This section is auto-generated from the help text for the planemo command
test
. This help message can be generated with planemo test
--help
.
Usage:
planemo test [OPTIONS] TOOL_PATH
Help
Run specified tool or workflow tests within Galaxy.
All referenced tools (by default all the tools in the current working directory) will be tested and the results quickly summarized.
To run these tests planemo needs a Galaxy instance to utilize, planemo
will search parent directories to see if any is a Galaxy instance
- but one can pick the Galaxy instance to use with the –galaxy_root
option or force planemo to download a disposable instance with the
--install_galaxy
flag.
In addition to to quick summary printed to the console - various detailed
output summaries can be configured. tool_test_output.html
(settable
via --test_output
) will contain a human consumable HTML report
describing the test run. A JSON file (settable via --test_output_json
and defaulting to tool_test_output.json
) will also be created. These
files can can be disabled by passing in empty arguments or globally by
setting the values default_test_output
and/or
default_test_output_json
in ~/.planemo.yml
to null
. For
continuous integration testing a xUnit-style report can be configured using
the --test_output_xunit
.
planemo uses temporarily generated config files and environment variables to attempt to shield this execution of Galaxy from manually launched runs against that same Galaxy root - but this may not be bullet proof yet so please careful and do not try this against production Galaxy instances.
Options:
--failed Re-run only failed tests. This command will
read tool_test_output.json to determine which
tests failed so this file must have been
produced with the same set of tool ids
previously.
--polling_backoff INTEGER Poll resources with an increasing interval
between requests. Useful when testing against
remote and/or production instances to limit
generated traffic.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--paste_test_data_paths / --no_paste_test_data_paths
By default Planemo will use or not use
Galaxy's path paste option to load test data
into a history based on the engine type it is
targeting. This can override the logic to
explicitly enable or disable path pasting.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
Select an engine to run or test artifacts such
as tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container or the CWL reference implementation
'cwltool' and 'toil' be selected.
--non_strict_cwl Disable strict validation of CWL.
--no-container, --no_container If cwltool engine is used, disable Docker
container usage.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--install_tool_dependencies / --no_install_tool_dependencies
Turn on installation of tool dependencies
using classic toolshed packages.
--install_resolver_dependencies / --no_install_resolver_dependencies
Skip installing tool dependencies through
resolver (e.g. conda).
--install_repository_dependencies / --no_install_repository_dependencies
Skip installing the repository dependencies.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_admin_key TEXT Admin key to use with external Galaxy engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--history_name TEXT Name to give a Galaxy history, if one is
created.
--history_id TEXT Send the results of the run to the history
with the provided ID. A history with this ID
must exist.
--no_wait After invoking a job or workflow, do not wait
for completion.
--help Show this message and exit.
test_reports
command
This section is auto-generated from the help text for the planemo command
test_reports
. This help message can be generated with planemo test_reports
--help
.
Usage:
planemo test_reports [OPTIONS] FILE_PATH
Help
Generate human readable tool test reports.
Creates reports in various formats (HTML, text, markdown) from the structured test output (tool_test_output.json).
Options:
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--help Show this message and exit.
tool_init
command
This section is auto-generated from the help text for the planemo command
tool_init
. This help message can be generated with planemo tool_init
--help
.
Usage:
planemo tool_init [OPTIONS]
Help
Generate tool outline from given arguments. Options:
-i, --id TEXT Short identifier for new tool (no whitespace)
-f, --force Overwrite existing tool if present.
-t, --tool FILE Output path for new tool (default is <id>.xml)
-n, --name TEXT Name for new tool (user facing)
--version TEXT Tool XML version.
-d, --description TEXT Short description for new tool (user facing)
-c, --command TEXT Command potentially including cheetah variables
()(e.g. 'seqtk seq -A $input > $output')
--example_command TEXT Example to command with paths to build Cheetah
template from (e.g. 'seqtk seq -A 2.fastq >
2.fasta'). Option cannot be used with --command,
should be used --example_input and --example_output.
--example_input TEXT For use with --example_command, replace input file
(e.g. 2.fastq with a data input parameter).
--example_output TEXT For use with --example_command, replace input file
(e.g. 2.fastq with a tool output).
--named_output TEXT Create a named output for use with command block for
example specify --named_output=output1.bam and then
use '-o $output1' in your command block.
--input TEXT An input description (e.g. input.fasta)
--output TEXT An output location (e.g. output.bam), the Galaxy
datatype is inferred from the extension.
--help_text TEXT Help text (reStructuredText)
--help_from_command TEXT Auto populate help from supplied command.
--doi TEXT Supply a DOI (http://www.doi.org/) easing citation
of the tool for Galxy users (e.g. 10.1101/014043).
--cite_url TEXT Supply a URL for citation.
--test_case For use with --example_commmand, generate a tool
test case from the supplied example.
--macros Generate a macros.xml for reuse across many tools.
--version_command TEXT Command to print version (e.g. 'seqtk --version')
--requirement TEXT Add a tool requirement package (e.g. 'seqtk' or
'seqtk@1.68').
--container TEXT Add a Docker image identifier for this tool.
--cwl Build a CWL tool instead of a Galaxy tool.
--autopygen TEXT Option for automatic generation of tool file, from
python source code that uses argparse. Parameter is
a path to source file containing definition of the
parser
--help Show this message and exit.
training_fill_data_library
command
This section is auto-generated from the help text for the planemo command
training_fill_data_library
. This help message can be generated with planemo training_fill_data_library
--help
.
Usage:
planemo training_fill_data_library [OPTIONS] TOOL_PATH
Help
Build training template from workflow. Options:
--topic_name TEXT Name (directory name) of the topic to create or in which
a tutorial should be created or updates [required]
--tutorial_name TEXT Name (directory name) of the tutorial to modify
[required]
--zenodo_link TEXT Zenodo URL with the input data
--help Show this message and exit.
training_generate_from_wf
command
This section is auto-generated from the help text for the planemo command
training_generate_from_wf
. This help message can be generated with planemo training_generate_from_wf
--help
.
Usage:
planemo training_generate_from_wf [OPTIONS] TOOL_PATH
Help
Create tutorial skeleton from workflow. Options:
--topic_name TEXT Name (directory name) of the topic to create
or in which a tutorial should be created or
updates [required]
--tutorial_name TEXT Name (directory name) of the tutorial to
modify [required]
--workflow PATH Workflow of the tutorial (locally)
--galaxy_url TEXT URL of a Galaxy instance with the workflow
--galaxy_api_key TEXT API key on the Galaxy instance with the
workflow
--workflow_id TEXT ID of the workflow on the Galaxy instance
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.
training_init
command
This section is auto-generated from the help text for the planemo command
training_init
. This help message can be generated with planemo training_init
--help
.
Usage:
planemo training_init [OPTIONS] TOOL_PATH
Help
Build training template from workflow. Options:
--topic_name TEXT Name (directory name) of the topic to create
or in which a tutorial should be created or
updates [required]
--topic_title TEXT Title of the topic to create
--topic_summary TEXT Summary of the topic
--topic_target [use|admin-dev|instructors]
Target audience for the topic
--tutorial_name TEXT Name (directory name) of the tutorial to
create or to modify
--tutorial_title TEXT Title of the tutorial
--hands_on Add hands-on for the new tutorial
--slides Add slides for the new tutorial
--workflow PATH Workflow of the tutorial (locally)
--galaxy_url TEXT URL of a Galaxy instance with the workflow
--galaxy_api_key TEXT API key on the Galaxy instance with the
workflow
--workflow_id TEXT ID of the workflow on the Galaxy instance
--zenodo_link TEXT Zenodo URL with the input data
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.
upload_data
command
This section is auto-generated from the help text for the planemo command
upload_data
. This help message can be generated with planemo upload_data
--help
.
Usage:
planemo upload_data [OPTIONS] RUNNABLE_PATH_OR_ID JOB_PATH NEW_JOB_PATH
Help
Planemo command for uploading data to an external Galaxy server.
% planemo upload_data wf.ga wf-job.yml new-wf-job.yml --profile profile
Running this subcommand requires a workflow file or identifier
and a job file, just as for planemo run
. In addition, a third
argument is required, for the location of a new job file which
Planemo will write. The data will be uploaded to the specified
external Galaxy server and the job file will be recreated at the
specified location, with all instances of path
or location
for input datasets and collections replaced by galaxy_id
. The
new job file can then be used to run the workflow separately from
the already completed data upload.
Options:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--tags TEXT Comma-separated list of tags to add to the
created history.
--help Show this message and exit.
workflow_convert
command
This section is auto-generated from the help text for the planemo command
workflow_convert
. This help message can be generated with planemo workflow_convert
--help
.
Usage:
planemo workflow_convert [OPTIONS] WORKFLOW_PATH_OR_ID
Help
Convert Format 2 workflows to native Galaxy workflows, and vice-versa. Options:
-f, --force Overwrite existing files if present.
-o, --output FILE
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.
workflow_edit
command
This section is auto-generated from the help text for the planemo command
workflow_edit
. This help message can be generated with planemo workflow_edit
--help
.
Usage:
planemo workflow_edit [OPTIONS] WORKFLOW_PATH_OR_ID
Help
Open a synchronized Galaxy workflow editor. Options:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--docker_run_extra_arguments TEXT
Extra arguments to pass to docker run.
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--port INTEGER Port to serve Galaxy on (default is 9090).
--host TEXT Host to bind Galaxy to. Default is 127.0.0.1
that is restricted to localhost connections
for security reasons set to 0.0.0.0 to bind
Galaxy to all ports including potentially
publicly accessible ones.
--engine [galaxy|docker_galaxy|external_galaxy]
Select an engine to serve artifacts such as
tools and workflows. Defaults to a local
Galaxy, but running Galaxy within a Docker
container.
--non_strict_cwl Disable strict validation of CWL.
--docker_galaxy_image TEXT Docker image identifier for docker-galaxy-
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--daemon Serve Galaxy process as a daemon.
--pid_file FILE Location of pid file is executed with
--daemon.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
may not prevent a workflow from successfully
executing.
--install_prebuilt_client / --no_install_prebuilt_client
Install a pre-built client from npm. Turn this
off you need access to visualizations.
--skip_client_build Do not build Galaxy client when serving
Galaxy.
--shed_install / --no_shed_install
By default Planemo will attempt to install
repositories needed for workflow testing. This
may not be appropriate for production servers
and so this can disabled by calling planemo
with --no_shed_install.
--help Show this message and exit.
workflow_job_init
command
This section is auto-generated from the help text for the planemo command
workflow_job_init
. This help message can be generated with planemo workflow_job_init
--help
.
Usage:
planemo workflow_job_init [OPTIONS] WORKFLOW_PATH_OR_ID
Help
Initialize a Galaxy workflow job description for supplied workflow.
Be sure to your lint your workflow with workflow_lint
before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
Jobs can be run with the planemo run command (planemo run workflow.ga job.yml
).
Planemo run works with Galaxy tools and CWL artifacts (both tools and workflows)
as well so this command may be renamed to to job_init at something along those
lines at some point.
Options:
-f, --force Overwrite existing files if present.
-o, --output FILE
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--from_invocation / --from_uri Build a workflow test or job description from
an invocation ID run on an external Galaxy.A
Galaxy URL and API key must also be specified.
This allows test data to be downloadedand
inputs and parameters defined automatically.
Alternatively, the default is to build
thedescriptions from a provided workflow URI.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--help Show this message and exit.
workflow_lint
command
This section is auto-generated from the help text for the planemo command
workflow_lint
. This help message can be generated with planemo workflow_lint
--help
.
Usage:
planemo workflow_lint [OPTIONS] TARGET
Help
Check workflows for syntax errors and best practices. Options:
--report_level [all|warn|error]
--report_xunit PATH Output an XUnit report, useful for CI testing
--fail_level [warn|error]
-s, --skip TEXT Comma-separated list of lint tests to skip
(e.g. passing --skip 'citations,xml_order'
would skip linting of citations and best-
practice XML ordering.
--iwc Check workflows directory with the standards
of iwc
--help Show this message and exit.
workflow_test_init
command
This section is auto-generated from the help text for the planemo command
workflow_test_init
. This help message can be generated with planemo workflow_test_init
--help
.
Usage:
planemo workflow_test_init [OPTIONS] WORKFLOW_PATH_OR_ID
Help
Initialize a Galaxy workflow test description for supplied workflow.
Be sure to lint your workflow with workflow_lint
before calling this
to ensure inputs and outputs comply with best practices that make workflow
testing easier.
Options:
-f, --force Overwrite existing files if present.
-o, --output FILE
--split_test / --no_split_test Write workflow job and test definitions to
separate files.
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--from_invocation / --from_uri Build a workflow test or job description from
an invocation ID run on an external Galaxy.A
Galaxy URL and API key must also be specified.
This allows test data to be downloadedand
inputs and parameters defined automatically.
Alternatively, the default is to build
thedescriptions from a provided workflow URI.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--help Show this message and exit.
workflow_test_on_invocation
command
This section is auto-generated from the help text for the planemo command
workflow_test_on_invocation
. This help message can be generated with planemo workflow_test_on_invocation
--help
.
Usage:
planemo workflow_test_on_invocation [OPTIONS] TEST.YML INVOCATION_ID
Help
Run defined tests against existing workflow invocation. Options:
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine. [required]
--galaxy_user_key TEXT User key to use with external Galaxy engine.
[required]
--test_index INTEGER Select which test to check. Counting starts at
1
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_markdown_minimal PATH
Output test report (Minimal markdown style -
jost the table)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--help Show this message and exit.
workflow_upload
command
This section is auto-generated from the help text for the planemo command
workflow_upload
. This help message can be generated with planemo workflow_upload
--help
.
Usage:
planemo workflow_upload [OPTIONS] TARGET
Help
Upload workflows to github organization. Options:
--namespace TEXT Organization or username under which to create or update
workflow repository. Must be a valid github username or
organization
--github_branch TEXT GitHub branch to use for the action. Default is main.
--dry_run Don't execute action, show preview of action.
--help Show this message and exit.