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 miniforge 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|postgres_singularity|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', 'postgres_docker' , and
postgres_singularity 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. . Use postgres_singularity to have
Planemo run postgres using
singularity/apptainer. 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.
--postgres-storage-location TEXT
storage path for postgres database, used for
local singularity postgres.
--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.