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2020-01-21gnu: Use HTTPS for (gnu packages bioinformatics) home pages....* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython) (discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary) (sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore) (gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer) (pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-01-21gnu: r-gage: Update home page....* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update. Tobias Geerinckx-Rice
2020-01-21gnu: sra-tools: Update home page....* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update. Tobias Geerinckx-Rice
2020-01-21gnu: raxml: Update home page....* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update. Tobias Geerinckx-Rice
2020-01-21gnu: prodigal: Update home page....* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page. Tobias Geerinckx-Rice
2020-01-21gnu: miso: Update home page....* gnu/packages/bioinformatics.scm (miso)[home-page]: Update. Tobias Geerinckx-Rice
2020-01-21gnu: grit: Update home page....* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code repository as home page. Tobias Geerinckx-Rice
2020-01-21gnu: express-beta-diversity: Update home page....The original is not coming back: <https://github.com/dparks1134/ExpressBetaDiversity/issues/11>. * gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]: Use source code repository as home page. Tobias Geerinckx-Rice
2020-01-21gnu: dendropy: Update home page....* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update. Tobias Geerinckx-Rice
2020-01-21gnu: Use HTTPS for bioconductor.org....* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS. * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked, r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno, r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise. * gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise. Tobias Geerinckx-Rice
2020-01-19gnu: edirect: Use HTTPS home page....* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-01-16gnu: kentutils: Build with OpenSSL 1.0....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to OPENSSL-1.0. Marius Bakke
2020-01-16gnu: r-delayedarray: Update to 0.12.2....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2. Ricardo Wurmus
2020-01-16gnu: r-iranges: Update to 2.20.2....* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2. Ricardo Wurmus
2020-01-16gnu: r-s4vectors: Update to 0.24.2....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2. Ricardo Wurmus
2020-01-16gnu: r-biocstyle: Update to 2.14.4....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4. Ricardo Wurmus
2020-01-09gnu: smithwaterman: Update to 0.0.0-2.2610e25....* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25. [arguments]: Add make-flags to build static library. Adjust custom 'install phase to install static library. Efraim Flashner
2020-01-09gnu: vcflib: Update to 1.0.1....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1. [source]: Download using url-fetch. [native-inputs]: Sort alphabetically. Move perl, python ... [inputs]: ... to here. [arguments]: Add make-flags. Update custom 'build phase. (tabixpp-freebayes): Remove variable. (freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes. Efraim Flashner
2020-01-09gnu: fastahack: Update to 1.0.0....* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0. Efraim Flashner
2020-01-09gnu: Add intervaltree....* gnu/packages/bioinformatics.scm (intervaltree): New variable. (vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source. Efraim Flashner
2020-01-09gnu: tabixpp: Update to 1.1.0....* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.0. [source]: Add snippet to remove vendored library. [arguments]: Adjust custom 'build phase to fix INCLUDES. Efraim Flashner
2020-01-09gnu: bwa: Install static library....* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static library. Efraim Flashner
2020-01-03gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition....This fixes the bug which prevented uglify-js from being defined properly, and cascaded back to all Common Lisp packages. * gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz. * gnu/packages/cran.scm: Use lisp-xyz module. * gnu/packages/javascript.scm (uglify-js): Move from here... * gnu/packages/lisp-xyz.scm: ... To here. * gnu/packages/web.scm: Replace javascript module with lisp-xyz. * guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module. Pierre Neidhardt
2019-12-27gnu: r-topgo: Update to 2.38.1....* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1. Ricardo Wurmus
2019-12-27gnu: r-summarizedexperiment: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1. Ricardo Wurmus
2019-12-27gnu: r-delayedarray: Update to 0.12.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1. Ricardo Wurmus
2019-12-27gnu: r-biocparallel: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1. Ricardo Wurmus
2019-12-27gnu: r-shortread: Update to 1.44.1....* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1. Ricardo Wurmus
2019-12-23gnu: python-bbknn: Update to 1.3.6....* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.3.6. [arguments]: Disable tests until migration to python-scikit-learn. [propgated-inputs]: Remove python-faiss, python-scanpy. [propgated-inputs]: Add python-scipy, python-umap-learn. Brett Gilio
2019-12-23gnu: tophat: Build with GCC 5...* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5. (tophat)[inputs]: Reorder alphabetically the dependencies. (tophat)[home-page]: Swapp to https. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Mădălin Ionel Patrașcu
2019-12-21gnu: fastx-toolkit: Build with GCC 6...* gnu/packages/bioinformatics.scm (fastx-toolkit)[native-inputs]: Add gcc-6. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Mădălin Ionel Patrașcu
2019-12-20gnu: r-scater: Update to 1.14.6....* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6. Ricardo Wurmus
2019-12-17gnu: Add libsbml....* gnu/packages/bioinformatics.scm (libsbml): New variable. Ricardo Wurmus
2019-12-17gnu: r-seurat: Update to 3.1.2....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2. Ricardo Wurmus
2019-12-16gnu: python-gffutils: Update description....* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow paragraph and fix spelling of SQLite. Ricardo Wurmus
2019-12-16gnu: Add python-gffutils....* gnu/packages/bioinformatics.scm (python-gffutils): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2019-12-16gnu: python-pyfaidx: Update to 0.5.7....* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7. Mădălin Ionel Patrașcu
2019-12-15gnu: r-genefilter: Update to 1.68.0....* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0. [propagated-inputs]: Remove r-s4vectors and add r-biocgenerics. Ricardo Wurmus
2019-12-15gnu: r-deseq2: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0. Ricardo Wurmus
2019-12-15gnu: r-dexseq: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0. Ricardo Wurmus
2019-12-15gnu: r-annotationforge: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0. Ricardo Wurmus
2019-12-15gnu: r-rbgl: Update to 1.62.1....* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1. Ricardo Wurmus
2019-12-15gnu: r-gseabase: Update to 1.48.0....* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0. Ricardo Wurmus
2019-12-15gnu: r-category: Update to 2.52.1....* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1. Ricardo Wurmus
2019-12-15gnu: r-gostats: Update to 2.52.0....* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0. Ricardo Wurmus
2019-12-15gnu: r-shortread: Update to 1.44.0....* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0. Ricardo Wurmus
2019-12-15gnu: r-systempiper: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0. Ricardo Wurmus
2019-12-15gnu: r-grohmm: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.20.0. Ricardo Wurmus
2019-12-15gnu: r-biocviews: Update to 1.54.0....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0. Ricardo Wurmus
2019-12-15gnu: r-biocstyle: Update to 2.14.2....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2. Ricardo Wurmus
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