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path: root/gn/packages/bioinformatics.scm
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2020-01-09gn: edirect-gn: Use an alternate xtract.LinuxEfraim Flashner
2019-12-22Revert "Removed python-science and crates-io to build with latest guix"...This reverts commit adbf2a07ea0274f718b60ef5ba3a7786360552d1. Efraim Flashner
2019-12-22Removed python-science and crates-io to build with latest guixpjotrp
2019-12-18wip: singlecellrshiny is not yet completeEfraim Flashner
2019-12-10gn: Remove r-qtl2....This package is now upstream. Efraim Flashner
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....* gn/packages/boost.scm (boost-static): Remove variable. Efraim Flashner
2019-11-25gn: Remove sdsl-lite-gn....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. Efraim Flashner
2019-11-24gn: Add graphaligner, mummer....* gn/packages/bioinformatics.scm (graphaligner, mummer): New variables. Efraim Flashner
2019-11-21gn: rn6-assembly-error-app: Use pngs from static location....* gn/packages/bioinformatics.scm (rn6-assembly-error-app): Search for pngs in gn-rshiny'S $HOME rather than in /gnu/store. Efraim Flashner
2019-11-19gn: Add seqwish.Efraim Flashner
2019-10-16gn: bxd-power-calculator-app: Provide alternate locations for csv file....* 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. Efraim Flashner
2019-10-16gn: bxd-power-calculator-app: Bind to port 3978.Efraim Flashner
2019-10-16gn: rn6-assembly-error-app: Create launcher script....* 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. Efraim Flashner
2019-10-16gn: Add bxd-power-calculator-app....* gn/packages/bioinformatics.scm (bxd-power-calculator-app): New variable. Efraim Flashner
2019-09-29gn: rn6-assembly-error-app: Update to 0.12....* gn/packages/bioinformatics.scm (rn6-assembly-error-app): Update to 0.12. [license]: Update license. Efraim Flashner
2019-09-26gn: Add rn6-assembly-error-app....* gn/packages/bioinformatics.scm (rn6-assembly-error-app): New variable. Efraim Flashner
2019-09-11gn: Add qctool....* gn/packages/bioinformatics.scm (qctool): New variable. Efraim Flashner
2019-09-11gnu: Add bamaddrg....* gn/packages/bioinformatics.scm (bamaddrg): New variable. Efraim Flashner
2019-09-03gn: Add ngmlr, svim....* gn/packages/bioinformatics.scm (ngmlr, svim): New variables. Efraim Flashner
2019-09-02gn: Add sniffles....* gn/packages/bioinformatics.scm (sniffles): New variable. Efraim Flashner
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 typo...* gn/packages/bioinformatics.scm (edirect-gn)[supported-systems]: Replace atom with list. Efraim Flashner
2019-08-21gn: edirect-gn: Add native-search-path....* gn/packages/bioinformatics.scm (edirect-gn)[native-search-paths]: New field. Efraim Flashner
2019-08-21gn: edirect-gn: Install missing binary....* 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. Efraim Flashner
2019-08-20gn: Add custom edirect packageEfraim Flashner
2019-08-05gn: varscan: Fix build....* gn/packages/bioinformatics.scm (varscan)[arguments]: Disable tests. Update all custom phases. [home-page]: Use https. [description]: Add it. Efraim Flashner
2019-08-05gn: Remove some duplicate packagesEfraim Flashner
2019-08-05gn: contra: Remove bundled source....* gn/packages/bioinformatics.scm (contra)[source]: Add snippet to remove bundled sources. Efraim Flashner
2019-08-05gn: contra: Update package definition....* gn/packages/bioinformatics.scm (contra)[arguments]: Update custom 'install phase. Efraim Flashner
2019-08-05gn: contra: Update source uri....* gn/packages/bioinformatics.scm (contra)[source]: Update to new folder structure. Efraim Flashner
2019-08-05gn: pindel: Update package definition....* gn/packages/bioinformatics.scm (pindel)[arguments]: Use 'invoke' when possible. Parameterize custom 'check phase. Efraim Flashner
2019-08-05gn: pindel: Don't use unstable tarball....* gn/packages/bioinformatics.scm (pindel)[source]: Download using 'git-fetch'. Efraim Flashner
2019-08-05gn: Add edirect-11....* gn/packages/bioinformatics.scm (edirect-11): New variable. Efraim Flashner
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 viability...- removed r-wcna and r-preprocesscore as they are in Guix now pjotrp
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
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