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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

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jmchilton
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Continuation of pull request here #492.

nturaga and others added 30 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
Removed bioconda_path requirement
4732a87
@nturaga
Multiple libraries not being parsed, need to skip getopt as part of r…
1bf6a38 
…equirements for bioconda
@nturaga
Working version of rscript_parse for GCC 2016
bcddac0
@jmchilton
Merge remote-tracking branch 'galaxyproject/master' into add_bioc_too…
3ad38e6 
…l_init

Conflicts:
	requirements.txt
@nturaga
Merge upstream updates to branch
dcd1f80
@jmchilton
Remove unused variabe in bioc_tool_builder.py.
6c47093
@jmchilton
Import instead of copy and paste TOOL_TEMPLATE in btb.py...
afb9585
@jmchilton
Import instead of copy and paste MACROS_TEMPLATE in btb.py...
157f129
@jmchilton
Import more stuff from tool_builder in btb instead copy/paste.
12637f3
@jmchilton
Opps pull UrlCitation out of both files in last refactoring.
d276b08
@jmchilton
More de-duplicating between btb and tb.
2a322c3
@jmchilton
Remove unused Container class in btb.
d2c7501
@jmchilton
Remove now unused import in btb.py.
fae22f0
@nturaga
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nturaga commented Oct 24, 2016 •
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@jmchilton Can you take a look at why the planemo tests fail? If it just a style issue, i'll fix em. Is there any other blocker?

@jmchilton
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There are definitely style issues and they should be fixed. There is also a pyaml import issue that prevents tests from loading:

    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/travis/build/galaxyproject/planemo/planemo/commands/cmd_brew_init.py", line 7, in <module>
    from planemo.cli import command_function
  File "/home/travis/build/galaxyproject/planemo/planemo/cli.py", line 11, in <module>
    from planemo.galaxy import profiles
  File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/__init__.py", line 5, in <module>
    from .config import galaxy_config
  File "/home/travis/build/galaxyproject/planemo/planemo/galaxy/config.py", line 24, in <module>
    from planemo.conda import build_conda_context
  File "/home/travis/build/galaxyproject/planemo/planemo/conda.py", line 17, in <module>
    from planemo.bioconda_scripts import bioconductor_skeleton
  File "/home/travis/build/galaxyproject/planemo/planemo/bioconda_scripts/bioconductor_skeleton.py", line 14, in <module>
    import pyaml
ImportError: No module named pyaml

There may be more problems also.

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nturaga commented Oct 25, 2016

Will fix now!

@nturaga nturaga changed the title [WIP] Bioconductor Support Bioconductor Support Oct 26, 2016
@nturaga nturaga self-assigned this Oct 26, 2016
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nturaga commented Oct 26, 2016

@jmchilton can you take a look ?

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nturaga commented Nov 10, 2016

@jmchilton Any update on this?

jmchilton
jmchilton commented Nov 11, 2016
View reviewed changes
planemo/tool_builder.py
@@ -734,6 +734,7 @@ def __init__(self, input_description, name=None, example=False):

def __str__(self):
template = '<param type="data" name="{0}" format="{1}" />'
self.datatype = self.datatype.split(".")[-1]
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Is this line needed? It seems broken.

@jmchilton jmchilton merged commit 140c6bb into galaxyproject:master Nov 14, 2016
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5 participants
@jmchilton @nturaga @bgruening @dannon @malloryfreeberg