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2019-12-04gn: Add r-qtl2.Efraim Flashner
2019-12-03gn: Adjust import for upstream changesEfraim Flashner
2019-12-02gn: edirect-gn: Install more files.Efraim Flashner
2019-11-25gn: seqwish: Link against dynamic sdsl-lite library.Efraim Flashner
2019-11-25gn: boost-static: Upstreamed.Efraim Flashner
* gn/packages/boost.scm (boost-static): Remove variable.
2019-11-25gn: Remove sdsl-lite-gn.Efraim Flashner
We can use libdivsufsort from (gnu packages bioinformatics). * gn/packages/bioinformatics.scm (sdsl-lite-gn): Remove variable. (seqwish, graphaligner)[inputs]: Remove sdsl-lite-gn. Add sdsl-lite, libdivsufsort. [arguments]: Adjust for change in inputs.
2019-11-24gn: Add graphaligner, mummer.Efraim Flashner
* gn/packages/bioinformatics.scm (graphaligner, mummer): New variables.
2019-11-21gn: rn6-assembly-error-app: Use pngs from static location.Efraim Flashner
* gn/packages/bioinformatics.scm (rn6-assembly-error-app): Search for pngs in gn-rshiny'S $HOME rather than in /gnu/store.
2019-11-19gn: Add seqwish.Efraim Flashner
2019-10-16gn: bxd-power-calculator-app: Provide alternate locations for csv file.Efraim Flashner
* gn/packages/bioinformatics.scm (bxd-power-calculator-app)[inputs]: Download csv datasets file from archive.org. Also note its location in IPFS should it become necessary later.
2019-10-16gn: bxd-power-calculator-app: Bind to port 3978.Efraim Flashner
2019-10-16gn: rn6-assembly-error-app: Create launcher script.Efraim Flashner
* gn/packages/bioinformatics.scm (rn6-assembly-error-app)[arguments]: Remove some library substitutions. Fix location of png directory. Create launcher script. [inputs]: Add r-minimal. Move r-ggplot2, r-shiny ... [propagated-inputs]: ... to here. Add r.
2019-10-16gn: Add bxd-power-calculator-app.Efraim Flashner
* gn/packages/bioinformatics.scm (bxd-power-calculator-app): New variable.
2019-09-29gn: rn6-assembly-error-app: Update to 0.12.Efraim Flashner
* gn/packages/bioinformatics.scm (rn6-assembly-error-app): Update to 0.12. [license]: Update license.
2019-09-26gn: Add rn6-assembly-error-app.Efraim Flashner
* gn/packages/bioinformatics.scm (rn6-assembly-error-app): New variable.
2019-09-11gn: Add qctool.Efraim Flashner
* gn/packages/bioinformatics.scm (qctool): New variable.
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
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