added receipe for bdgenomics.mango

[akmorrow13]

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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).

[biocondabot]

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[biocondabot]

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	show curl "https://78864-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/mango%3A0.0.5--py_0.tar.gz" | gzip -dc | docker load

[dpryan79]

You'll need to add the various bdgenomics dependencies.

[npavlovikj]

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]

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

[heuermh]

@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]

@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.

[dpryan79]

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]

@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).