870
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Ran 16 Dec 2015 07:31AM UTC

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Build # 870

Build Type

push

travis-ci

Committed by

jmchilton

Commit Message

Implement conda support.

Planemo Conda Commands:

 - conda_init: Install a conda runtime.
 - conda_install: Takes in a tool or list 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.

Implement a conda dependency resolver. Has a variety of options:

 - 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.
 - Above options for planemo - prefix, exec, debug.

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_.

Run Details

Jobs

ID	Job ID	Ran
1	870.1 (TOX_ENV=py27-lint)	16 Dec 2015 07:31AM UTC	Travis Job 870.1
2	870.2 (TOX_ENV=py34-lint)	16 Dec 2015 07:32AM UTC	Travis Job 870.2
3	870.3 (TOX_ENV=py27-lint-readme)	16 Dec 2015 07:32AM UTC	Travis Job 870.3

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