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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
2019-08-15gn: hyphy: Update to 2.5.0.Efraim Flashner
* gn/packages/hyphy.scm (hyphy): Update to 2.5.0. [source]: Download using 'git-fetch'. [inputs]: Add curl, openssl. [arguments]: Add test-target.
2019-08-13gn: Clean up some cratesEfraim Flashner
2019-08-1242 crates upstreamedEfraim Flashner
2019-08-12gn: mongodb upstreamedEfraim Flashner
2019-08-12gn: add missing module importsEfraim Flashner
2019-08-09gn: openfbya: Clean up package.Efraim Flashner
* gn/packages/openfyba.scm (openfyba)[source]: Don't use unstable tarball. [arguments]: Use 'boostrap phase to replace 'boostrap phase. Adjust for change in source.
2019-08-09gn: 4store upstreamedEfraim Flashner
2019-08-06gn: clFFT: Update to 2.12.2.Efraim Flashner
* gn/packages/arrayfire.scm (clFFT): Update to 2.12.2.
2019-08-06gn: Fix building arrayfire.Efraim 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 upstream packagesEfraim Flashner
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.
2019-08-05gn: Add ratspub.Efraim Flashner
* gn/packages/ratspub.scm (ratspub): New variable.
2019-08-04gn: rust-qtlreaper: Update with upstream changes.Efraim Flashner
* gn/packages/genenetwork.scm (rust-qtlreaper)[arguments]: Remove custom phases.
2019-08-04bnw: Build binaries.Efraim Flashner
* gn/packages/bnw.scm (bnw)[build-system]: Use gnu-build-system. [arguments]: Adjust accordingly. [native-inputs]: Remove source. [inputs]: Remove bash-minimal, add rmath-standalone.
2019-08-01Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformaticsPjotr Prins
2019-07-30minor rust updatesEfraim Flashner
2019-07-30gn: minor rust updatesEfraim Flashner
2019-07-29gn: python-shellescape: Clean up package definition.Efraim Flashner
* gn/packages/python.scm (python-shellescape): Re-indent. [source]: Use pypi uri. [inputs]: Move python-setuptools ... [native-inputs]: ... to here. [license]: Use 'license' prefix.
2019-07-29gn: python-subprocess32: Correctly mark as version 3.5.3.Efraim Flashner
* gn/packages/python.scm (python-subprocess32): Re-indent. [version]: Correct to 3.5.3, which is what the source was downloading. [source]: Use pypi uri.
2019-07-29gn: python-typing-extensions: Clean up package definition.Efraim Flashner
* gn/packages/python.scm (python-typing-extensions): Re-indent. [source]: Use pypi uri.
2019-07-29gn: python-bagit: Clean up package definition.Efraim Flashner
* gn/packages/python.scm (python-bagit)[source]: Use pypi uri. [synopsis, description]: Update.
2019-07-29gn: Add rust-qtlreaper and dependencies.Efraim Flashner
* gn/packages/genenetwork.scm (rust-qtlreaper): New variable. * gn/packages/crates-io.scm (~300 packages): New variables.
2019-07-22gn: bnw: Add javascript libraries.Efraim Flashner
* gn/packages/bnw.scm (bnw)[inputs]: Add web-jquery, web-font-awesome, javascript-cytoscape, javascript-cytoscape-2, javascript-dagre, javascript-lodash, javascript-cytoscape-dagre, javascript-cytoscape-panzoom, javascript-d3js-4, javascript-d3js-multi, javascript-canvas-toblob, javascript-filesaver. [arguments]: Add references to new inputs.
2019-07-22gn: Add javascript-filesaver.Efraim Flashner
* gn/packages/javascript.scm (javascript-filesaver): New variable.
2019-07-22gn: Add javascript-canvas-toblob.Efraim Flashner
* gn/packages/javascript.scm (javascript-canvas-toblob): New variable.
2019-07-22gn: Add javascript-d3js-multi.Efraim Flashner
* gn/packages/javascript.scm (javascript-d3js-multi): New variable.
2019-07-22gn: Add javascript-d3js-4.Efraim Flashner
* gn/packages/javascript.scm (javascript-d3js-4): New variable.
2019-07-22gn: Add javascript-d3js.Efraim Flashner
* gn/packages/javascript.scm (javascript-d3js): New variable.
2019-07-22gn: Add javascript-lodash.Efraim Flashner
* gn/packages/javascrpt.scm (javascript-lodash): New variable.
2019-07-22gn: Add font-awesome.Efraim Flashner
* gn/packages/web.scm (font-awesome): New variable.
2019-07-22gn: Add javascript-cytoscape-dagre.Efraim Flashner
* gn/packages/javascript.scm (javascript-cytoscape-dagre): New variable.
2019-07-22gn: Add javascript-dagre.Efraim Flashner
* gn/packages/javascript.scm (javascript-dagre): New variable.
2019-07-22gn: bnw: Patch '/usr/bin/dot' references.Efraim Flashner
* gn/packages/bnw.scm (bnw): Add substitute* to patch '/usr/bin/dot' calls with store graphviz references.
2019-07-21gn: Add javascript-cytoscape-popper.Efraim Flashner
* gn/packages/web.scm (javascript-cytoscape-popper): New variable.
2019-07-21gn: Add javascript-qtip2.Efraim Flashner
* gn/packages/javascript.scm (javascript-qtip2): New variable.
2019-07-21gn: web-bootstrap-native: Clean up package.Efraim Flashner
* gn/packages/web.scm (web-bootstrap-native): Re-indent. [arguments]: Clean up build.
2019-07-21gn: web-bootstrap: Update to 4.3.1.Efraim Flashner
* gn/packages/web.scm (web-bootstrap): Update to 4.3.1.
2019-07-21gn: web-bootstrap: Clean up package.Efraim Flashner
* gn/packages/web.scm (web-bootstrap)[source]: Download using 'git-fetch'. [native-inputs]: Remove unzip. [arguments]: Adjust accordingly. [home-page]: Use https.
2019-07-21gn: web-jquery: Update to 3.4.1.Efraim Flashner
* gn/packages/web.scm (web-jquery): Update to 3.4.1.
2019-07-21gn: web-jquery: Clean up package.Efraim Flashner
* gn/packages/web.scm (web-jquery)[source]: Download with 'git-fetch'. [native-inputs]: Remove unzip. [arguments]: Adjust accordingly. [home-page]: Use https. [synopsis]: Update synopsis. [description]: Flesh out description.
2019-07-21gn: javascript-datatables: Update to 1.10.19.Efraim Flashner
* gn/packages/javascript.scm (javascript-datatables): Update to 1.10.19. [source]: Download using git-fetch. [native-inputs]: Remove gzip, tar. [inputs]: Move javascript-cytoscape ... [propagated-inputs]: ... to here. [arguments]: Adjust accordingly. [home-page]; Update home-page. [synopsis]: Update synopsis. [description]: Flesh out description.
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