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Bioconductor Support #570

Merged
merged 80 commits into from
Nov 14, 2016
Merged

Bioconductor Support #570

merged 80 commits into from
Nov 14, 2016

Commits on Apr 29, 2016

  1. Added bioconductor_skeleton and cmd_bioc_tool_init.py

    @nturaga
    nturaga committed Apr 29, 2016
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Commits on May 5, 2016

  1. reshuffle some code

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Commits on May 14, 2016

  1. This makes the bioconductor_skeleton.py compatible with python 2

    @nturaga
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Commits on May 27, 2016

  1. Add bioconda helper functions, 

    1. Write bioconda recipe
2. clone bioconda repo

Add command line utility, to initiate bioconda recipe when given package name. "conda_recipe_init"
    @nturaga
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Commits on May 31, 2016

  1. Add bioconda path to bioc_tool_init , deprecated commit, do NOT use.

    @nturaga
    nturaga committed May 31, 2016
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  2. minor changes

    @nturaga
    nturaga committed May 31, 2016
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  3. Update requirements for bioc_tool_init work; it'd be nice to eliminat… 

    …e some of the very lightly used deps here though.
    @dannon
    dannon committed May 31, 2016
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  4. Merge pull request #1 from dannon/add_bioc_tool_init 

    Update requirements for bioc_tool_init work; it'd be nice to eliminat…
    @nturaga
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  5. Get version from bioconda

    @nturaga
    nturaga committed May 31, 2016
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  6. typo fix bioconda

    @dannon
    dannon committed May 31, 2016
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  7. Merge pull request #2 from dannon/biconda_bioconda 

    typo fix bioconda
    @nturaga
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  8. IO error

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Commits on Jun 2, 2016

  1. Removed print statements, need to add package_url, package_help from … 

    …requirements directly
    @nturaga
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  2. Add help from bioconductor directly

    @nturaga
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  3. Removed print statements, this commit, now has working versions of cm… 

    …d_bioc_tool_init, and bioc_tool_builder.
    @nturaga
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  4. rename command line tool, conda_recipe_init to bionconductor_conda_re… 

    …cipe_init
    @nturaga
    nturaga committed Jun 2, 2016
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  5. another name change

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Commits on Jun 7, 2016

  1. Removed bioconda_path requirement

    @nturaga
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Commits on Jun 25, 2016

  1. Multiple libraries not being parsed, need to skip getopt as part of r… 

    …equirements for bioconda
    @nturaga
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Commits on Jun 26, 2016

  1. Working version of rscript_parse for GCC 2016

    @nturaga
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Commits on Jun 27, 2016

  1. Merge remote-tracking branch 'galaxyproject/master' into add_bioc_too… 

    …l_init

Conflicts:
	requirements.txt
    @jmchilton
    jmchilton committed Jun 27, 2016
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Commits on Sep 16, 2016

  1. Merge upstream updates to branch

    @nturaga
    nturaga committed Sep 16, 2016
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Commits on Sep 19, 2016

  1. Remove unused variabe in bioc_tool_builder.py.

    @jmchilton
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  2. Import instead of copy and paste TOOL_TEMPLATE in btb.py...

    @jmchilton
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  3. Import instead of copy and paste MACROS_TEMPLATE in btb.py...

    @jmchilton
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  4. Import more stuff from tool_builder in btb instead copy/paste.

    @jmchilton
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  5. Opps pull UrlCitation out of both files in last refactoring.

    @jmchilton
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  6. More de-duplicating between btb and tb.

    @jmchilton
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  7. Remove unused Container class in btb.

    @jmchilton
    jmchilton committed Sep 19, 2016
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  8. Remove now unused import in btb.py.

    @jmchilton
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  9. Remove more duplication between tb.py and btb.py.

    @jmchilton
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  10. Remove more duplication between tb.py and btb.py.

    @jmchilton
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  11. Remove duplication in bioc id option.

    @jmchilton
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  12. Remove duplication related to tool init options and names.

    @jmchilton
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  13. De-duplication of tool init name handling options.

    @jmchilton
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  14. Remove duplicate tool init handling for three more options.

    @jmchilton
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  15. De-duplicate four more tool init options.

    @jmchilton
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  16. Eliminate more copy-paste betweeen cmd_bti and cmd_ti.

    @jmchilton
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  17. De-duplication of 4 more options between cbti and cti.

    @jmchilton
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  18. Fix unused import in cmd_tool_init.

    @jmchilton
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  19. De-duplicate the usage of three more options between tool init flavors.

    @jmchilton
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  20. Capture more of tool_init's options in planemo/options.py. 

    These four are as of yet unshared with bioc_tool_init or shared in slightly different forms.
    @jmchilton
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  21. Reuse more of tool init's options with different help in bioc_ti.

    @jmchilton
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  22. Rearrange comments related to tool init commands.

    @jmchilton
    jmchilton committed Sep 19, 2016
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  23. Fix two problems I introduced in planemo/options.py.

    @jmchilton
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  24. Merge branch 'master' into add_bioc_features

    @nturaga
    nturaga committed Sep 19, 2016
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  25. remove container options

    @nturaga
    nturaga committed Sep 19, 2016
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  26. add updates to bioconductor_skeleton.py file, remove unused dependencies

    @nturaga
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Commits on Sep 20, 2016

  1. replace - to _, to follow planemo conventions, next version can have … 

    …required longterm changes to switch to hyphens
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Commits on Sep 21, 2016

  1. Put bioconductor_skeleton.py in a new directory called 'bioconda_scri… 

    …pts' as the folder 'xml' interferes with import (xml.sax), add modules to conda.py to make it run
    @nturaga
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  2. Merge branch 'master' into add_bioc_features

    @nturaga
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Commits on Oct 12, 2016

  1. merge upstream/master to add_bioc_features

    @nturaga
    nturaga committed Oct 12, 2016
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  2. conda add requirements

    @nturaga
    nturaga committed Oct 12, 2016
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  3. add git

    @nturaga
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Commits on Oct 17, 2016

  1. fixed tool naming in cmd_bioc_tool_init.py

    @malloryfreeberg
    malloryfreeberg committed Oct 17, 2016
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  2. Merge pull request #3 from malloryfreeberg/add_bioc_features_mallory 

    fixed tool naming in cmd_bioc_tool_init.py
    @nturaga
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Commits on Oct 24, 2016

  1. Bioconductor tool builder edits

    @malloryfreeberg
    malloryfreeberg committed Oct 24, 2016
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  2. This patch fixes the missing $ signs in front of the parameters

    @nturaga
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  3. Merge pull request #5 from malloryfreeberg/add_bioc_features_mallory 

    Add bioc features mallory
    @nturaga
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  4. Prepare version 0.34.1.

    @jmchilton @nturaga
    jmchilton authored and nturaga committed Oct 24, 2016
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  5. Version 0.34.1

    @jmchilton @nturaga
    jmchilton authored and nturaga committed Oct 24, 2016
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  6. Starting work on 0.35.0

    @jmchilton @nturaga
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  7. moved bioconda recipe generation to conda_recipes.py

    @nturaga
    nturaga committed Oct 24, 2016
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Commits on Oct 25, 2016

  1. Adds the option --rversion so the user to specify an R version. 

    It also takes care of some flake8 issues, along with adding the requirements in the right order.
The order of the requirements in flipped in Line 116 where there is a FIXME tag. This is to
be dealt with later.
    @nturaga
    nturaga committed Oct 25, 2016
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  2. Fix lint issues from travis.

    @nturaga
    nturaga committed Oct 25, 2016
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  3. Reordered bioc_skeleton

    @nturaga
    nturaga committed Oct 25, 2016
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  4. Flake 8 fixes

    @nturaga
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  5. typo in pyaml

    @nturaga
    nturaga committed Oct 25, 2016
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  6. Fix linting issues

    @nturaga
    nturaga committed Oct 25, 2016
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  7. Py3 lint fix

    @nturaga
    nturaga committed Oct 25, 2016
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  8. Py3 unused variable

    @nturaga
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Commits on Oct 26, 2016

  1. Importanize the order of packages for Py27 lint check

    @nturaga
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  2. i100 errors on py27

    @nturaga
    nturaga committed Oct 26, 2016
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  3. Class too complex issue should be resolved with this commit

    @nturaga
    nturaga committed Oct 26, 2016
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  4. pylint

    @nturaga
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  5. Pylint 27

    @nturaga
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  6. Final pylint 2.7 issue

    @nturaga
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  7. Fix doctest for bioconductor_skeleton.py

    @nturaga
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Commits on Nov 8, 2016

  1. merge master into feature branch

    @nturaga
    nturaga committed Nov 8, 2016
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Commits on Nov 11, 2016

  1. add pyyaml to requirements file

    @nturaga
    nturaga committed Nov 11, 2016
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