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added receipe for bdgenomics.mango #17960

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merged 11 commits into from
Oct 23, 2019
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akmorrow13
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@akmorrow13 akmorrow13 commented Oct 8, 2019

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  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

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biocondabot bot commented Oct 8, 2019

Welcome to Bioconda, @akmorrow13! Thank you for opening your first pull request! As you're new to Bioconda, please read through our documentation about contributing recipes. If you need help, please ping one of the following teams:

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biocondabot bot commented Oct 9, 2019

Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
noarch mango-0.0.5-py_0.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages in noarch:
    conda install -c https://78864-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
    

Docker image(s) built:

Package Tag Install with docker
mango 0.0.5--py_0
showcurl "https://78864-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/mango%3A0.0.5--py_0.tar.gz" | gzip -dc | docker load

@dpryan79
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dpryan79 commented Oct 9, 2019

You'll need to add the various bdgenomics dependencies.

@npavlovikj
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The current error message is:

19:18:14 BIOCONDA INFO (OUT) /opt/conda/conda-bld/mango_1571252876304/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/mango-submit: line 64: /opt/conda/conda-bld/mango_1571252876304/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/find-mango-assembly.sh: No such file or directory

Looks like "mango-submit" is using "find-mango-assembly.sh" which is not symlinked to $BINARY_HOME and thus not found. I would suggest you to symlink the other scripts in "/bin" in "build.sh" as well (or the whole "/bin" directory all together), or change the location of SCRIPT_DIR.

@dpryan79
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I've fixed the initial set of problems, though this points out some real oddities in how the software is structured.

@heuermh
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heuermh commented Oct 20, 2019

@dpryan79

...though this points out some real oddities in how the software is structured.

We ran into similar issues with how conda breaks apart our tarballs with symlinks in the Bioconda recipe for adam. The workarounds and patches there are still not entirely satisfactory, see e.g. bigdatagenomics/adam#2225. Do you have any suggestions as to how to better structure our release artifacts?

@akmorrow13
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@dpryan79 would you know why $SP_DIR is set correctly during the initial test phase but is no longer set correctly during the mulled-build build-and-test phase? This description of conda variables says that SP_DIR should also be set during test.

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There's no conda activate run inside the container, since the base environment contains the package. Given that, no environment variables will be set.

@dpryan79
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@heuermh The occasional symlink shouldn't be an issue. The structure problem with the packages seems to be that the jar files aren't being properly installed with pip. They should be treated as data files (to use python lingo).

@dpryan79 dpryan79 merged commit a9faca6 into bioconda:master Oct 23, 2019
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4 participants