From 3f4ab44604ad40ea66b178e28eb3a99e11874383 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 5 May 2016 10:32:07 -0400 Subject: [PATCH] Update command docs. --- docs/commands.rst | 4 +++ docs/commands/conda_env.rst | 31 ++++++++++++++++++++ docs/commands/conda_init.rst | 34 +++++++++++++++++++++ docs/commands/conda_install.rst | 26 +++++++++++++++++ docs/commands/cwl_run.rst | 50 ++++++++++++++++++++++++++++--- docs/commands/docker_build.rst | 2 +- docs/commands/docs.rst | 20 +++++++++++++ docs/commands/lint.rst | 4 +-- docs/commands/serve.rst | 50 ++++++++++++++++++++++++++++--- docs/commands/shed_lint.rst | 1 - docs/commands/shed_serve.rst | 52 +++++++++++++++++++++++++++++++-- docs/commands/shed_test.rst | 16 ++++++++-- docs/commands/syntax.rst | 1 - docs/commands/test.rst | 42 +++++++++++++++++++++++--- docs/commands/tool_factory.rst | 50 ++++++++++++++++++++++++++++--- 15 files changed, 357 insertions(+), 26 deletions(-) create mode 100644 docs/commands/conda_env.rst create mode 100644 docs/commands/conda_init.rst create mode 100644 docs/commands/conda_install.rst create mode 100644 docs/commands/docs.rst diff --git a/docs/commands.rst b/docs/commands.rst index 9d692ba54..206d39b66 100644 --- a/docs/commands.rst +++ b/docs/commands.rst @@ -10,12 +10,16 @@ documentation describes these commands. .. include:: commands/brew.rst .. include:: commands/brew_env.rst .. include:: commands/brew_init.rst +.. include:: commands/conda_env.rst +.. include:: commands/conda_init.rst +.. include:: commands/conda_install.rst .. include:: commands/config_init.rst .. include:: commands/cwl_run.rst .. include:: commands/cwl_script.rst .. include:: commands/dependency_script.rst .. include:: commands/docker_build.rst .. include:: commands/docker_shell.rst +.. include:: commands/docs.rst .. include:: commands/lint.rst .. include:: commands/normalize.rst .. include:: commands/project_init.rst diff --git a/docs/commands/conda_env.rst b/docs/commands/conda_env.rst new file mode 100644 index 000000000..c7ae23339 --- /dev/null +++ b/docs/commands/conda_env.rst @@ -0,0 +1,31 @@ + +``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** + +Source output to activate a conda environment for this tool. + + % . <(planemo conda_env bowtie2.xml) + % which bowtie2 + TODO_PLACE_PATH_HERE + +**Options**:: + + + --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_ensure_channels TEXT Ensure conda is configured with specified comma + separated list of channels. + --help Show this message and exit. + diff --git a/docs/commands/conda_init.rst b/docs/commands/conda_init.rst new file mode 100644 index 000000000..9fcde2880 --- /dev/null +++ b/docs/commands/conda_init.rst @@ -0,0 +1,34 @@ + +``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. + +**Options**:: + + + --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_ensure_channels TEXT Ensure conda is configured with specified comma + separated list of channels. + --help Show this message and exit. + diff --git a/docs/commands/conda_install.rst b/docs/commands/conda_install.rst new file mode 100644 index 000000000..44068f5c7 --- /dev/null +++ b/docs/commands/conda_install.rst @@ -0,0 +1,26 @@ + +``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] TOOL_PATH + +**Help** + +Install conda packages for tool requirements. +**Options**:: + + + --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_ensure_channels TEXT Ensure conda is configured with specified comma + separated list of channels. + --help Show this message and exit. + diff --git a/docs/commands/cwl_run.rst b/docs/commands/cwl_run.rst index f108d28dc..97ac3da93 100644 --- a/docs/commands/cwl_run.rst +++ b/docs/commands/cwl_run.rst @@ -23,10 +23,18 @@ Planemo command for running CWL tools and jobs. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -34,7 +42,11 @@ Planemo command for running CWL tools and jobs. 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. --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 @@ -47,12 +59,42 @@ Planemo command for running CWL tools and jobs. --dependency_resolvers_config_file PATH Dependency resolver configuration for Galaxy to target. - --tool_dependency_dir DIRECTORY - Tool dependency dir 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. + --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_ensure_channels TEXT Ensure conda is configured with specified + comma separated list of channels. + --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 Conda dependency resolution for Galaxy will + auto install will attempt to install requested + but missing packages. + --conda_auto_init Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --profile TEXT Location of pid file is executed with + --daemon. + --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. + --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. + --daemon Serve Galaxy process as a daemon. + --pid_file TEXT Location of pid file is executed with + --daemon. --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 diff --git a/docs/commands/docker_build.rst b/docs/commands/docker_build.rst index fb9b07fb2..3a67ffd91 100644 --- a/docs/commands/docker_build.rst +++ b/docs/commands/docker_build.rst @@ -12,7 +12,7 @@ This section is auto-generated from the help text for the planemo command **Help** -Builds (and optionally caches Docker images) for tool Dockerfiles. +Build (and optionally cache Docker images) for tool Dockerfiles. 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 diff --git a/docs/commands/docs.rst b/docs/commands/docs.rst new file mode 100644 index 000000000..178eb00fb --- /dev/null +++ b/docs/commands/docs.rst @@ -0,0 +1,20 @@ + +``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 the Planemo documentation in a web browser. +**Options**:: + + + --help Show this message and exit. + diff --git a/docs/commands/lint.rst b/docs/commands/lint.rst index f7e8695b4..dd922e641 100644 --- a/docs/commands/lint.rst +++ b/docs/commands/lint.rst @@ -12,9 +12,7 @@ This section is auto-generated from the help text for the planemo command **Help** -Check specified tool(s) for common errors and adherence to best -practices. - +Check tools for common errors and adherence to best practices. **Options**:: diff --git a/docs/commands/serve.rst b/docs/commands/serve.rst index e89a2b6d9..163943ffb 100644 --- a/docs/commands/serve.rst +++ b/docs/commands/serve.rst @@ -39,10 +39,18 @@ instances. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -50,7 +58,11 @@ instances. 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. --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 @@ -63,12 +75,42 @@ instances. --dependency_resolvers_config_file PATH Dependency resolver configuration for Galaxy to target. - --tool_dependency_dir DIRECTORY - Tool dependency dir 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. + --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_ensure_channels TEXT Ensure conda is configured with specified + comma separated list of channels. + --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 Conda dependency resolution for Galaxy will + auto install will attempt to install requested + but missing packages. + --conda_auto_init Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --profile TEXT Location of pid file is executed with + --daemon. + --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. + --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. + --daemon Serve Galaxy process as a daemon. + --pid_file TEXT Location of pid file is executed with + --daemon. --cwl Configure Galaxy for use with CWL tool. (this option is experimental and will be replaced when and if CWL support is merged into diff --git a/docs/commands/shed_lint.rst b/docs/commands/shed_lint.rst index a3ea9d5db..c3057b719 100644 --- a/docs/commands/shed_lint.rst +++ b/docs/commands/shed_lint.rst @@ -14,7 +14,6 @@ This section is auto-generated from the help text for the planemo command Check a Tool Shed repository for common problems. - With the ``--tools`` flag, this command lints actual Galaxy tools in addition to tool shed artifacts. diff --git a/docs/commands/shed_serve.rst b/docs/commands/shed_serve.rst index d7f93dbd1..aeb17dd3d 100644 --- a/docs/commands/shed_serve.rst +++ b/docs/commands/shed_serve.rst @@ -47,10 +47,18 @@ logged into and explored interactively. mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -58,13 +66,53 @@ logged into and explored interactively. 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. --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. + --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_ensure_channels TEXT Ensure conda is configured with specified + comma separated list of channels. + --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 Conda dependency resolution for Galaxy will + auto install will attempt to install requested + but missing packages. + --conda_auto_init Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --profile TEXT Location of pid file is executed with + --daemon. + --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. + --pid_file TEXT Location of pid file is executed with + --daemon. --skip_dependencies Do not install shed dependencies as part of repository installation. --help Show this message and exit. diff --git a/docs/commands/shed_test.rst b/docs/commands/shed_test.rst index e24333f1a..d7a82eb3b 100644 --- a/docs/commands/shed_test.rst +++ b/docs/commands/shed_test.rst @@ -48,10 +48,18 @@ This command requires the target to be version 15.07 or newer. mappings defined ~/.planemo.yml. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -59,7 +67,11 @@ This command requires the target to be version 15.07 or newer. 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. --job_config_file PATH Job configuration file for Galaxy to target. + --tool_dependency_dir DIRECTORY + Tool dependency dir for Galaxy to target. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) diff --git a/docs/commands/syntax.rst b/docs/commands/syntax.rst index 7829d8920..e689944a0 100644 --- a/docs/commands/syntax.rst +++ b/docs/commands/syntax.rst @@ -13,7 +13,6 @@ This section is auto-generated from the help text for the planemo command **Help** Open tool config syntax wiki page in a web browser. - **Options**:: diff --git a/docs/commands/test.rst b/docs/commands/test.rst index 3f2768183..567a9249a 100644 --- a/docs/commands/test.rst +++ b/docs/commands/test.rst @@ -49,10 +49,18 @@ please careful and do not try this against production Galaxy instances. previously. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -60,19 +68,45 @@ please careful and do not try this against production Galaxy instances. 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. --job_config_file PATH Job configuration file for Galaxy to target. + --tool_dependency_dir DIRECTORY + Tool dependency dir for Galaxy to target. --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. - --tool_dependency_dir DIRECTORY - Tool dependency dir 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. + --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_ensure_channels TEXT Ensure conda is configured with specified + comma separated list of channels. + --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 Conda dependency resolution for Galaxy will + auto install will attempt to install requested + but missing packages. + --conda_auto_init Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --profile TEXT Location of pid file is executed with + --daemon. + --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. --update_test_data Update test-data directory with job outputs (normally written to directory --job_output_files if specified.) diff --git a/docs/commands/tool_factory.rst b/docs/commands/tool_factory.rst index 59436e1b7..a95f2fd86 100644 --- a/docs/commands/tool_factory.rst +++ b/docs/commands/tool_factory.rst @@ -24,10 +24,18 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011. --galaxy_root DIRECTORY Root of development galaxy directory to execute command with. - --galaxy_sqlite_database DIRECTORY - Preseeded Galaxy sqlite database to target. + --galaxy_database_seed PATH Preseeded Galaxy sqlite database to target. --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 @@ -35,7 +43,11 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011. 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. --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 @@ -48,11 +60,41 @@ http://www.ncbi.nlm.nih.gov/pubmed/23024011. --dependency_resolvers_config_file PATH Dependency resolver configuration for Galaxy to target. - --tool_dependency_dir DIRECTORY - Tool dependency dir 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. + --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_ensure_channels TEXT Ensure conda is configured with specified + comma separated list of channels. + --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 Conda dependency resolution for Galaxy will + auto install will attempt to install requested + but missing packages. + --conda_auto_init Conda dependency resolution for Galaxy will + auto install conda itself using miniconda if + not availabe on conda_prefix. + --profile TEXT Location of pid file is executed with + --daemon. + --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. + --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. + --daemon Serve Galaxy process as a daemon. + --pid_file TEXT Location of pid file is executed with + --daemon. --help Show this message and exit.