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2020-03-22gn: Upstream edirect-gnEfraim Flashner
2020-03-12gn: edirect-gn: Fix edirect-gnEfraim Flashner
This commit does many things: Adjust for upstream update. Fix the error not allowing us to download new data. Use self-compiled binaries instead of downloading from upstream. Install more scripts. Wrap all the programs and scripts so they can work in a pureenvironment.
2020-03-12gn: edirect-gn: Build go packages from source.Efraim Flashner
2020-03-12gn: Add missing module import.Efraim Flashner
2020-03-12gn: Add grocsvs and dependenciesEfraim Flashner
2020-03-11gn: singlecellrshiny: Update home-page.Efraim Flashner
2020-03-05gn: singlecellrshiny is readyEfraim Flashner
2020-03-04WIP: singlecellrshinyEfraim Flashner
2020-03-03WIP: incomplete update to singlecellrshiny.Efraim Flashner
2020-02-18gn: Update edirect-gn to match upstream update.Efraim Flashner
2020-02-16gn: edirect-gn: Wrap more binariesEfraim Flashner
2020-02-05gn: edirect binary seems to have been modified againEfraim Flashner
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"Efraim Flashner
This reverts commit adbf2a07ea0274f718b60ef5ba3a7786360552d1.
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.Efraim Flashner
This package is now upstream.
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.
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