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Bioconductor Support #570

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merged 80 commits into from Nov 14, 2016

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jmchilton commented Sep 21, 2016

Continuation of pull request here #492.

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jmchilton commented on scripts/bioconductor_skeleton.py in 8b735ed May 6, 2016

I would from planemo.io import info instead and use that.

nturaga and others added some commits May 14, 2016

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"
Update requirements for bioc_tool_init work; it'd be nice to eliminat…
…e some of the very lightly used deps here though.
Merge pull request #1 from dannon/add_bioc_tool_init
Update requirements for bioc_tool_init work; it'd be nice to eliminat…
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nturaga commented Oct 24, 2016

@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?

@nturaga nturaga added high priority and removed high priority labels Oct 24, 2016

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jmchilton commented Oct 25, 2016

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 added some commits Oct 25, 2016

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 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?

@@ -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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jmchilton Nov 11, 2016

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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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