use readlink to properly source source dir

[mtdeguzis]

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.

[AmplabJenkins]

Can one of the admins verify this patch?

[heuermh]

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?

[heuermh]

Jenkins, test this please.

[mtdeguzis]

@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.

[AmplabJenkins]

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.

[akmorrow13]

This does not work on Mac. Generates error:

readlink: illegal option -- f
usage: readlink [-n] [file ...]
usage: dirname path

[mtdeguzis]

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

[heuermh]

Closing as WontFix