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Fixed failed installation of minimac4 in gwas.sif #196

Merged
merged 10 commits into from
Oct 17, 2023
Merged

Fixed failed installation of minimac4 in gwas.sif #196

merged 10 commits into from
Oct 17, 2023

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espenhgn
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@espenhgn espenhgn commented Sep 1, 2023 •
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Fixes #195
Fixes #198

Changes proposed in this pull request:

  • Adds tools beagle, duohmm, eagle, shapeit5, switchError to gwas.sif
  • Added tests
  • Updated Dockerfile and shell scripts and rebuilt gwas.sif container file
  • Removed unused docker/scripts/install_miniconda.sh script

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  • I've read and followed all steps in the Making a pull request
    section of the CONTRIBUTING docs.
  • I've updated or added any relevant docstrings following the syntax described in the
    Writing docstrings section of the CONTRIBUTING docs.
  • If this PR fixes a bug, I've added a test that will fail without my fix.
  • If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

@espenhgn espenhgn changed the title Espenhgn/issue195 Fixed failed installation of minimac4 in gwas.sif Sep 1, 2023
@espenhgn espenhgn added the bug-fix fixes a bug label Sep 1, 2023
@espenhgn espenhgn requested a review from ofrei September 1, 2023 10:26
@espenhgn espenhgn mentioned this pull request Sep 13, 2023
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@espenhgn espenhgn marked this pull request as draft September 13, 2023 09:57
@espenhgn espenhgn marked this pull request as ready for review September 14, 2023 08:14
@espenhgn
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@ofrei, this should be good to go. As you have experience with this undocumented switchError software, perhaps you have a better idea of testing it.
With Eagle, I had some issues including a memcpy.o object file from a corresponding .cpp file during the build, but it looks like the system one got included instead.

espenhgn
espenhgn commented Oct 17, 2023
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Will merge as is.

@espenhgn espenhgn merged commit 00f7b51 into main Oct 17, 2023
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@espenhgn espenhgn deleted the espenhgn/issue195 branch October 17, 2023 08:49
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Add additional phasign and impute software gwas.sif: test_gwas_minimac4 is failing
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