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Cannot find `find-adam-assembly.sh` in bioconda build #1862

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heuermh opened this Issue Jan 5, 2018 · 2 comments

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@heuermh
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heuermh commented Jan 5, 2018

@fnothaft might need help debugging this one. The bioconda install splits the bin and package directories.

I thought the patches should no longer be necessary, because we rolled in the # Find original directory of this script, resovling symlinks block somewhere, but perhaps I am mistaken?

https://github.com/bioconda/bioconda-recipes/pull/7203/files

See
https://travis-ci.org/bioconda/bioconda-recipes/jobs/325551375

+ /bin/bash -x -e /opt/conda/conda-bld/adam_1515176451401/test_tmp/run_test.sh
+ adam-submit --help
/opt/conda/conda-bld/adam_1515176451401/_t_env/bin/adam-submit:
line 54: /opt/conda/conda-bld/adam_1515176451401/_t_env/bin/find-adam-assembly.sh:
No such file or directory
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fnothaft commented Jan 5, 2018

I would patch so that you've got set -x -v in all the scripts and see how far you can get.

@heuermh heuermh added this to the 0.24.0 milestone Jan 6, 2018

@heuermh heuermh self-assigned this Jan 6, 2018

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heuermh commented Jan 6, 2018

Looks like we still need those # Find original directory of this script blocks, at least for the bioconda recipe.

https://travis-ci.org/heuermh/bioconda-recipes/builds/325707349

@heuermh heuermh closed this Jan 6, 2018

@heuermh heuermh added this to Completed in Release 0.24.0 Jan 9, 2018

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