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gwas.sif: Include samtools, bedtools, liftOver; upgrade others #219

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ofrei opened this issue Jan 22, 2024 · 1 comment · Fixed by #222
Closed

gwas.sif: Include samtools, bedtools, liftOver; upgrade others #219

ofrei opened this issue Jan 22, 2024 · 1 comment · Fixed by #222
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@espenhgn
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enhancement New feature or request

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@ofrei
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ofrei commented Jan 22, 2024

Is your feature request related to a problem? Please describe.
samtools ( http://www.htslib.org/download/ ) package is developed by the same people as bcftools and htslib which we already have. It's useful (.e.g it include TABIX feature to index files, as required by some other packages - e.g. lokuszoom). Great if possible to include samtools in gwas.sif
@espenhgn espenhgn self-assigned this Jan 30, 2024
@espenhgn espenhgn changed the title Include samtools package in gwas.sif gwas.sif: Include samtools, bedtools, liftOver Feb 1, 2024
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espenhgn commented Feb 1, 2024 •
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Adding samtools together with bedtools (MIT license), liftOver (no-license - free for non-commercial use).
Also update remaining packages.

@espenhgn espenhgn changed the title gwas.sif: Include samtools, bedtools, liftOver gwas.sif: Include samtools, bedtools, liftOver; upgrade others Feb 1, 2024
espenhgn added a commit that referenced this issue Feb 2, 2024
@espenhgn
Include samtools package in gwas.sif
4b7a034 
Fixes #219
espenhgn added a commit that referenced this issue Feb 2, 2024
@espenhgn
Include samtools package in gwas.sif
a53654a 
Fixes #219
espenhgn added a commit that referenced this issue Feb 2, 2024
@espenhgn
gwas.sif: Include samtools, bedtools, liftOver; upgrade others
b7c6f26 
Fixes #219
@espenhgn espenhgn mentioned this issue Feb 2, 2024
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espenhgn added a commit that referenced this issue Feb 2, 2024
@espenhgn
gwas.sif: Include samtools, bedtools, liftOver; upgrade others
da6e4e2 
Fixes #219
@espenhgn espenhgn added the enhancement New feature or request label Feb 5, 2024
espenhgn added a commit that referenced this issue Feb 5, 2024
@espenhgn
gwas.sif: Add samtools, bedtools, liftOver, upgrade others (#222)
efad944 
* Include samtools package in gwas.sif
Fixes #219

* Include samtools package in gwas.sif
Fixes #219

* `gwas.sif`: Include samtools, bedtools, liftOver; upgrade others
Fixes #219

* rebuilt r.sif container

* updated changelog

* fix

* bump version file

* install GWAMA using apt

* rebuilt gwas.sif

* updated changelog
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gwas.sif: Add samtools, bedtools, liftOver, upgrade others comorment/containers
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@espenhgn @ofrei