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Update command docs.

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jmchilton committed May 5, 2016
1 parent 76d99b9 commit 3f4ab44604ad40ea66b178e28eb3a99e11874383
@@ -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
@@ -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.
@@ -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.
@@ -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.
@@ -23,18 +23,30 @@ 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
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.
--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
@@ -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
@@ -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.
@@ -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**::


@@ -39,18 +39,30 @@ 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
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.
--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
@@ -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.

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