galaxyproject / planemo / 879
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jmchilton 
Implement conda support.

This PR adds conda support to Planemo and via shared libraries to Galaxy in the form of new planemo commands providing a Galaxy tool-centric interface to conda for development and a Galaxy dependency resolver. Once the corresponding Galaxy PR is merged, the following command::

    planemo t --conda_dependency_resolution --conda_auto_install --conda_auto_init bwa_and_samtools.xml

Will test the supplied tool with only conda dependency resolution available. On startup, if Galaxy cannot find conda it will install it and for every dependency encountered it will attempt to find and install it on-demand.

Planemo Conda Commands:

 - conda_init: Install a conda runtime.
 - conda_install: Takes in a tool or set of tools and installs their requirements using conda in such a way that they can be recovered and reused by dependency resolution.
 - conda_env: Build isolated environment for a tool or set of tools.

Conda CLI Options:

Common options for conda commands in planemo.

  --conda_prefix: Location of conda runtime (defaults to ~/miniconda2).
  --conda_exec: Location of conda executble (defaults to <conda_prefix/bin/conda)
  --conda_debug: Flag, when enabled conda will execute with the --debug flag.
  --conda_ensure_channels: Ensure channels are available (defaults to "r,bioconda")

This PR implement a conda dependency resolver for Galaxy. This has a variety of options including:

 - copy_dependencies: This will copy dependencies into the working directory instead linking them - by passing --copy to conda create. Defaults to false.
 - auto_init: This will install conda if not avaiable on the system. Defaults to false.
 - auto_install: This will attempt to install packages for if they are not already installed.
 - Options mirroring the above for planemo - prefix, exec, debug, ensur_channels.

All these dependency resolution option can be set as attributes on the dependency resolver element in dependency_resolvers_conf.xml.sample, or in galaxy.ini with the prefix conda_.

Trying it out:

    $ planemo conda_init  # install conda
    $ # setup a couple tools for conda testing
    $ planemo project_init --templates conda_test
    $ cd conda_test
    $ # look at tool requirements and install packages
    $ planemo conda_install bwa.xml
    $ # Load up the tool's environment to explore interactively
    $ . <(planemo conda_env bwa.xml)
    (bwa)$ which bwa
    /home/john/miniconda2/envs/jobdepsdpzBA...186c6a5504767f9e7/bin/bwa
    $ conda_env_deactivate
    $ # Run the tool in galaxy using conda dependency resolution
    $ # All the tool and test case do is verify the dependency and version
    $ planemo t --conda_dependency_resolution bwa.xml
    $ # The galaxy dependency resolver can even install dependencies on demand
    $ planemo t --conda_dependency_resolution --conda_auto_install bwa_and_samtools.xml

3603 of 4511 relevant lines covered (79.87%)

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Jobs
ID Job ID Ran Files Coverage
1 879.1 (TOX_ENV=py27-lint) 0
Travis Job 879.1
2 879.2 (TOX_ENV=py34-lint) 0
Travis Job 879.2
3 879.3 (TOX_ENV=py27-lint-readme) 0
Travis Job 879.3
4 879.4 (TOX_ENV=py26) 0
79.87
 Travis Job 879.4
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