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] TOOL_URI JOB_PATHHelp
Planemo command for running tools and jobs.
% planemo run cat1-tool.cwl cat-job.jsonOptions:
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_database_seed PATH Preseeded Galaxy sqlite database to target.
--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 or
instance 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).
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker).
--job_config_file PATH Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--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 PATH
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 PATH Location of conda executable.
--conda_debug Enable more verbose conda logging.
--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_copy_dependencies Conda dependency resolution for Galaxy will
copy dependencies instead of attempting to
link them.
--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.
--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.
--output_directory, --outdir DIRECTORY
Where to store outputs of a 'run' task.
--output_json PATH Where to store JSON dictionary describing
outputs of a 'run' task.
--engine [galaxy|docker_galaxy|cwltool|toil|external_galaxy]
Select an engine to run or test aritfacts 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.
--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.
--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.
--help Show this message and exit.