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2019-09-11gnu: Add bamaddrg.Efraim Flashner
* gn/packages/bioinformatics.scm (bamaddrg): New variable.
2019-09-03gn: Add ngmlr, svim.Efraim Flashner
* gn/packages/bioinformatics.scm (ngmlr, svim): New variables.
2019-09-02gn: Add sniffles.Efraim Flashner
* gn/packages/bioinformatics.scm (sniffles): New variable.
2019-08-28gn: bioinformatics.scm: Clean up module imports.Efraim Flashner
2019-08-28gn: Remove some upstreamed packagesEfraim Flashner
2019-08-21gn: edirect-gn: Fix typoEfraim Flashner
* gn/packages/bioinformatics.scm (edirect-gn)[supported-systems]: Replace atom with list.
2019-08-21gn: edirect-gn: Add native-search-path.Efraim Flashner
* gn/packages/bioinformatics.scm (edirect-gn)[native-search-paths]: New field.
2019-08-21gn: edirect-gn: Install missing binary.Efraim Flashner
* gn/packages/bioinformatics.scm (edirect-gn)[arguments]: Install missing 'efetch' binary. Sort installed files alphabetically. Substitute call to 'exec perl' for all potentially affected files.
2019-08-20gn: Add custom edirect packageEfraim Flashner
2019-08-05gn: varscan: Fix build.Efraim Flashner
* gn/packages/bioinformatics.scm (varscan)[arguments]: Disable tests. Update all custom phases. [home-page]: Use https. [description]: Add it.
2019-08-05gn: Remove some duplicate packagesEfraim Flashner
2019-08-05gn: contra: Remove bundled source.Efraim Flashner
* gn/packages/bioinformatics.scm (contra)[source]: Add snippet to remove bundled sources.
2019-08-05gn: contra: Update package definition.Efraim Flashner
* gn/packages/bioinformatics.scm (contra)[arguments]: Update custom 'install phase.
2019-08-05gn: contra: Update source uri.Efraim Flashner
* gn/packages/bioinformatics.scm (contra)[source]: Update to new folder structure.
2019-08-05gn: pindel: Update package definition.Efraim Flashner
* gn/packages/bioinformatics.scm (pindel)[arguments]: Use 'invoke' when possible. Parameterize custom 'check phase.
2019-08-05gn: pindel: Don't use unstable tarball.Efraim Flashner
* gn/packages/bioinformatics.scm (pindel)[source]: Download using 'git-fetch'.
2019-08-05gn: Add edirect-11.Efraim Flashner
* gn/packages/bioinformatics.scm (edirect-11): New variable.
2018-10-14ldc: use ldc from mainlinepjotrp
2017-12-18Fixes against guix latestPjotr Prins
2017-10-23Renamed plink-ng package since it went into mainlinepjotrp
2017-07-16Guix moved zip to compressionpjotrp
2017-05-14Updating guixPjotr Prins
2017-03-16Moving gemma into its own modulepjotrp
2017-02-26Added comments on guix viabilitypjotrp
- removed r-wcna and r-preprocesscore as they are in Guix now
2017-02-23sambamba: moved into its own modulepjotrp
2017-02-23sambamba: updatedpjotrp
2017-02-23shunit2 packagepjotrp
2017-02-02Patching Druntime for sambambapjotrp
2017-01-29Shipped sambambapjotrp
2017-01-24sambamba: remove lz4 and rdmdpjotrp
2017-01-24Sambamba uses lz4.so, so the source download is no longer needed.pjotrp
Tested view of both BAM and CRAM works.
2017-01-24sambamba: make file builds with symbols by default and O2pjotrp
2017-01-21Debug version of sambambapjotrp
2017-01-20Sambamba: switched to guix makefilepjotrp
2016-12-25Recent sambambapjotrp
2016-09-29Move qtlreaper to genenetwork.scmpjotrp
2016-08-16Updated and fixed plink-nggn-stablepjotrp
2016-08-14Getting GN2 ready for new build - plink-ng is disabled and should not be ↵Pjotr Prins
built with atlas and lapack (FIXME)
2016-08-13python-pil: replace with pillowPjotr Prins
2016-05-15Merge branch 'gn-latest' of github.com:genenetwork/guix-bioinformatics into ↵Pjotr Prins
gn-latest
2016-05-15Disable ant - it gives an errorPjotr Prins
2016-05-11r-biocprocesscore has been updated.Dennis E. Mungai
This should fix the genenetwork2 build issue, as noted on IRC.
2016-03-30Merge branch 'master' of https://github.com/genenetwork/guix-bioinformaticsRoel Janssen
2016-03-23This runs with gn-stablepjotrp
2016-03-23Mergepjotrp
2016-03-23GN2 fixpjotrp
2016-03-23GN2 fixstablePjotr Prins
2016-03-23Fixed hashPjotr Prins
2016-03-18WIP: Add varscan.Roel Janssen
The JAR construction cannot contain a wild-card. That has to be fixed.
2016-03-16Add delly.Roel Janssen
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