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adam-submit cannot find assembly jar if installed as symlink #1616

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heuermh opened this issue Jul 21, 2017 · 1 comment
Closed

adam-submit cannot find assembly jar if installed as symlink #1616

heuermh opened this issue Jul 21, 2017 · 1 comment
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@heuermh
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@heuermh heuermh commented Jul 21, 2017

For better or worse, the bioconda guidelines are to install wrappers such as adam-submit and adam-shell as symlinks.

https://bioconda.github.io/guidelines.html#java

Our wrapper scripts cannot find the assembly jar if installed this way.

...
$ mkdir noarch
$ echo '{}' > noarch/repodata.json
$ bzip2 -k noarch/repodata.json
+ source /opt/conda/bin/activate /opt/conda/conda-bld/adam_1500624861141/_t_env
+ /bin/bash -x -e /opt/conda/conda-bld/adam_1500624861141/test_tmp/run_test.sh
+ adam-submit --help
ls: cannot access /opt/conda/conda-bld/adam_1500624861141/_t_env/adam-assembly/target: No such file or directory
Failed to find ADAM cli assembly in /opt/conda/conda-bld/adam_1500624861141/_t_env/adam-assembly/target.
You need to build ADAM before running this program.
@fnothaft
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@fnothaft fnothaft commented Jul 21, 2017

Resolved by e3fa6bf.

@fnothaft fnothaft closed this Jul 21, 2017
@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017
@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018
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