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[WIP] Add functionality for Bioconductor tool integration using Bioconda#492

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nturaga wants to merge 22 commits intogalaxyproject:masterfrom
nturaga:add_bioc_tool_init
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[WIP] Add functionality for Bioconductor tool integration using Bioconda#492
nturaga wants to merge 22 commits intogalaxyproject:masterfrom
nturaga:add_bioc_tool_init

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@nturaga nturaga commented Jun 2, 2016 •
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Hi,

I'm creating this pull request to make the addition of bioconductor tools easier. Two new commands have been added in the process,

  • bioc_conda_recipe_init : This allows to create a new bioconda recipe for bioconductor tools directly from planemo. It allows users to clone, update bioconda recipes if they choose.
    Example run:
planemo bioc_conda_recipe_init 
--clone
--update
--bioconda_path /Users/Documents/workspace/
--package_name ‘motifbreakR’
  • bioc_tool_init : This allows to create a bioconda recipe, if it does not already exist, and also create a tool definition file with the requirements satisfied, and pulls the "help" and "url" for the bioconductor tool directly.
    Example run:
planemo bioc_tool_init 
--name motifbreakR 
--id motifbreakR 
--requirement 'motifbreakR'
--bioconda_path /Users/Documents/workspace

This PR, can be tested with the above two examples. A third and more complete example is

planemo bioc_tool_init  
                    --name motifbreakR 
                    --id motifbreakR 
                    --requirement 'motifbreakR' 
                    --bioconda_path /Users/Documents/workspace 
                    --input 'variants.csv'  
                    --input 'motifdb.csv' 
                    --output 'motifbreakr.results' 
                    --example_command 'Rscript motifbreakR-sample-script.R  --input test-data/variants.csv  --input test-data/motifdb.csv --output test-data/output.csv'

nturaga and others added 17 commits April 29, 2016 16:30
@nturaga
Added bioconductor_skeleton and cmd_bioc_tool_init.py
8b735ed
@nturaga
reshuffle some code
ea68333
@nturaga
This makes the bioconductor_skeleton.py compatible with python 2
46ef4bc
@nturaga
Add bioconda helper functions,
4518033 
1. Write bioconda recipe
2. clone bioconda repo

Add command line utility, to initiate bioconda recipe when given package name. "conda_recipe_init"
@nturaga
Add bioconda path to bioc_tool_init , deprecated commit, do NOT use.
f33d6d7
@nturaga
minor changes
fbadda7
@dannon
Update requirements for bioc_tool_init work; it'd be nice to eliminat…
a0ee9f4 
…e some of the very lightly used deps here though.
@nturaga
Merge pull request #1 from dannon/add_bioc_tool_init
9980c76 
Update requirements for bioc_tool_init work; it'd be nice to eliminat…
@nturaga
Get version from bioconda
ce408c4
@dannon
typo fix bioconda
dc9e306
@nturaga
Merge pull request #2 from dannon/biconda_bioconda
f5ee6ef 
typo fix bioconda
@nturaga
IO error
b3ae28f
@nturaga
Removed print statements, need to add package_url, package_help from …
ed5ca75 
…requirements directly
@nturaga
Add help from bioconductor directly
461e187
@nturaga
Removed print statements, this commit, now has working versions of cm…
7d2d5c3 
…d_bioc_tool_init, and bioc_tool_builder.
@nturaga
rename command line tool, conda_recipe_init to bionconductor_conda_re…
28175eb 
…cipe_init
@nturaga
another name change
c63768d
@nturaga nturaga changed the title [WIP] Add functionality for Bioconductor tool integration using Bioconda Add functionality for Bioconductor tool integration using Bioconda Jun 3, 2016
@nturaga nturaga self-assigned this Jun 3, 2016
@nturaga nturaga mentioned this pull request Jun 3, 2016
Open
@nturaga nturaga changed the title Add functionality for Bioconductor tool integration using Bioconda [WIP] Add functionality for Bioconductor tool integration using Bioconda Jun 4, 2016
@jmchilton jmchilton mentioned this pull request Jun 9, 2016
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nturaga commented Sep 19, 2016 •
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This PR will be closed in favor of a new branch on my repo https://github.com/nturaga/planemo/tree/add_bioc_features

@jmchilton jmchilton mentioned this pull request Sep 21, 2016
Merged
@nturaga nturaga closed this Sep 21, 2016
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@nturaga @jmchilton @dannon