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use readlink to properly source source dir #2036

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@mtdeguzis
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commented Aug 29, 2018

Adam bin scripts assume you are in the right directory. In standing this up in a docker container, we wanted a central source code location + symlinks to the in scripts. Using readlink, you can easily obtain the real directory.

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commented Aug 29, 2018

Can one of the admins verify this patch?

@heuermh

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commented Aug 29, 2018

Hello @mtdeguzis, thank you for the pull request.

We officially support the Docker images created by the BioContainer project
https://quay.io/repository/biocontainers/adam?tab=tags

which are generated from the ADAM Bioconda package
https://bioconda.github.io/recipes/adam/README.html

We have to include a patch in the Bioconda recipe to properly handle symlinks (issue #1973); I wonder if you think this would also help with that issue?

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commented Aug 29, 2018

Jenkins, test this please.

@mtdeguzis

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commented Aug 29, 2018

@heuermh , sure I don't mind helping. I will take a look a that linked issue tomorrow. Running out of time today. If you have anything specific to note, that will help.

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commented Aug 29, 2018

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2800/
Test PASSed.

@heuermh heuermh requested a review from akmorrow13 Aug 30, 2018

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commented Aug 30, 2018

This does not work on Mac. Generates error:

readlink: illegal option -- f
usage: readlink [-n] [file ...]
usage: dirname path
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commented Sep 25, 2018

@akmorrow13 , noted. I'll see what I can do to make the patch universal.

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