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Revise Minimac4/bgenix installation in gwas.sif#64

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espenhgn merged 8 commits intomainfrom
fix-61
Oct 10, 2022
Merged

Revise Minimac4/bgenix installation in gwas.sif#64
espenhgn merged 8 commits intomainfrom
fix-61

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@espenhgn espenhgn commented Oct 4, 2022

Fixes #61

Changes proposed in this pull request:

  • Mainly makes sure that some build-time dependencies (Python stuff, cget utility) for Minimac4 is not included in the built containers
  • Adds a test for bgenix software

Before submitting

  • I've read and followed all steps in the Making a pull request
    section of the CONTRIBUTING docs.
  • If this PR adds a new feature, I've added tests that sufficiently cover my new functionality.

@espenhgn espenhgn added the enhancement New feature or request label Oct 4, 2022
@espenhgn espenhgn marked this pull request as draft October 4, 2022 14:06
@espenhgn espenhgn changed the title Revise Minimac4 install Revise Minimac4 installation in gwas.sif Oct 4, 2022
@espenhgn espenhgn changed the title Revise Minimac4 installation in gwas.sif Revise Minimac4/bgenix installation in gwas.sif Oct 5, 2022
@espenhgn espenhgn marked this pull request as ready for review October 5, 2022 10:34
@espenhgn espenhgn mentioned this pull request Oct 5, 2022
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ofrei
ofrei approved these changes Oct 10, 2022
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@espenhgn espenhgn merged commit d28f835 into main Oct 10, 2022
espenhgn added a commit that referenced this pull request Oct 10, 2022
@espenhgn
Squashed commit of the following:
5fad5c9 
commit d28f835
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:34:21 2022 +0200

    Revise Minimac4/bgenix installation in `gwas.sif` (#64)

    * dev branch squashing fix-39 onto main

    * revised Minimac4 installer script

    * add test that Minimac4 is installed in gwas.sif

    * minor edit to bgenix install+test

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated CHANGELOG

commit 90df3d0
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:31:40 2022 +0200

    Use Mambaforge for `python3.sif` builds  (#63)

    * dev branch squashing fix-39 onto main

    * download miniforge3

    * grap miniforge for appropriate platform

    * removed comments

    * install pyreadstat, xlrd, h5py from conda-forge

    * use mamba; mamba clean & pip cache purge

    * use Mambaforge

    * comment

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * src/scripts/install_miniconda3.sh -> src/scripts/install_mambaforge.sh

    * updated CHANGELOG.md

    * Minor updates to readme/changelog

commit 58edf7c
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 13:53:32 2022 +0200

    Remove libquadmath0 from builds (#60)

    * dev branch squashing fix-39 onto main

    * remove libquadmath0 from containers

    * KING seems fine without libquadmath0

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated changelog
espenhgn added a commit that referenced this pull request Oct 10, 2022
@espenhgn
Squashed commit of the following:
3f2292b 
commit a833a1a
Merge: 5fad5c9 d28f835
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 15:21:43 2022 +0200

    Merge branch 'main' into fix-43

commit 5fad5c9
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 13:17:38 2022 +0000

    Squashed commit of the following:

    commit d28f835
    Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
    Date:   Mon Oct 10 14:34:21 2022 +0200

        Revise Minimac4/bgenix installation in `gwas.sif` (#64)

        * dev branch squashing fix-39 onto main

        * revised Minimac4 installer script

        * add test that Minimac4 is installed in gwas.sif

        * minor edit to bgenix install+test

        * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

        * updated CHANGELOG

    commit 90df3d0
    Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
    Date:   Mon Oct 10 14:31:40 2022 +0200

        Use Mambaforge for `python3.sif` builds  (#63)

        * dev branch squashing fix-39 onto main

        * download miniforge3

        * grap miniforge for appropriate platform

        * removed comments

        * install pyreadstat, xlrd, h5py from conda-forge

        * use mamba; mamba clean & pip cache purge

        * use Mambaforge

        * comment

        * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

        * src/scripts/install_miniconda3.sh -> src/scripts/install_mambaforge.sh

        * updated CHANGELOG.md

        * Minor updates to readme/changelog

    commit 58edf7c
    Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
    Date:   Mon Oct 10 13:53:32 2022 +0200

        Remove libquadmath0 from builds (#60)

        * dev branch squashing fix-39 onto main

        * remove libquadmath0 from containers

        * KING seems fine without libquadmath0

        * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

        * updated changelog

commit d28f835
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:34:21 2022 +0200

    Revise Minimac4/bgenix installation in `gwas.sif` (#64)

    * dev branch squashing fix-39 onto main

    * revised Minimac4 installer script

    * add test that Minimac4 is installed in gwas.sif

    * minor edit to bgenix install+test

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated CHANGELOG

commit 90df3d0
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:31:40 2022 +0200

    Use Mambaforge for `python3.sif` builds  (#63)

    * dev branch squashing fix-39 onto main

    * download miniforge3

    * grap miniforge for appropriate platform

    * removed comments

    * install pyreadstat, xlrd, h5py from conda-forge

    * use mamba; mamba clean & pip cache purge

    * use Mambaforge

    * comment

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * src/scripts/install_miniconda3.sh -> src/scripts/install_mambaforge.sh

    * updated CHANGELOG.md

    * Minor updates to readme/changelog

commit 58edf7c
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 13:53:32 2022 +0200

    Remove libquadmath0 from builds (#60)

    * dev branch squashing fix-39 onto main

    * remove libquadmath0 from containers

    * KING seems fine without libquadmath0

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated changelog

commit 8bfa258
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Thu Oct 6 07:39:11 2022 +0000

    updated changelog

commit 6a23ec6
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 20:06:39 2022 +0000

    ubuntu 20.04 as base image

commit f75ea77
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 16:00:46 2022 +0000

    run apt-get clean after install

commit 74ae269
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:45:26 2022 +0000

    add test that python is installed in python3.sif

commit 825ba3e
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:25:24 2022 +0000

    rename test function

commit 4741840
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:25:14 2022 +0000

    bump base image to ubuntu:22.04

commit 9856755
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:09:01 2022 +0000

    fixed merge

commit ca2d649
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:06:31 2022 +0000

    squashed fix-42

commit 8ad61b9
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Wed Oct 5 12:05:01 2022 +0000

    squashed fix-46
@espenhgn espenhgn deleted the fix-61 branch October 10, 2022 14:29
espenhgn added a commit that referenced this pull request Oct 11, 2022
@espenhgn
Bump base image to Ubuntu:20.04 (#65)
411c220 
* squashed fix-46

* squashed fix-42

* fixed merge

* bump base image to ubuntu:22.04

* rename test function

* add test that python is installed in python3.sif

* run apt-get clean after install

* ubuntu 20.04 as base image

* updated changelog

* Squashed commit of the following:

commit d28f835
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:34:21 2022 +0200

    Revise Minimac4/bgenix installation in `gwas.sif` (#64)

    * dev branch squashing fix-39 onto main

    * revised Minimac4 installer script

    * add test that Minimac4 is installed in gwas.sif

    * minor edit to bgenix install+test

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated CHANGELOG

commit 90df3d0
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 14:31:40 2022 +0200

    Use Mambaforge for `python3.sif` builds  (#63)

    * dev branch squashing fix-39 onto main

    * download miniforge3

    * grap miniforge for appropriate platform

    * removed comments

    * install pyreadstat, xlrd, h5py from conda-forge

    * use mamba; mamba clean & pip cache purge

    * use Mambaforge

    * comment

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * src/scripts/install_miniconda3.sh -> src/scripts/install_mambaforge.sh

    * updated CHANGELOG.md

    * Minor updates to readme/changelog

commit 58edf7c
Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com>
Date:   Mon Oct 10 13:53:32 2022 +0200

    Remove libquadmath0 from builds (#60)

    * dev branch squashing fix-39 onto main

    * remove libquadmath0 from containers

    * KING seems fine without libquadmath0

    * usecases/bolt_out/example_3chr.frq,usecases/bolt_out/myld.l2.ldscore.gz: convert to Git LFS

    * updated changelog
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Software: install_minimac4.sh (from gwas repo) installs Python 2.7

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