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* gnu: smithwaterman: Update to 0.0.0-2.2610e25.Efraim Flashner2020-01-09
| | | | | | * 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.
* gnu: vcflib: Update to 1.0.1.Efraim Flashner2020-01-09
| | | | | | | | | | | * 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.
* gnu: fastahack: Update to 1.0.0.Efraim Flashner2020-01-09
| | | | * gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
* gnu: Add intervaltree.Efraim Flashner2020-01-09
| | | | | * gnu/packages/bioinformatics.scm (intervaltree): New variable. (vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
* gnu: tabixpp: Update to 1.1.0.Efraim Flashner2020-01-09
| | | | | | * 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.
* gnu: bwa: Install static library.Efraim Flashner2020-01-09
| | | | | * gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static library.
* gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition.Pierre Neidhardt2020-01-03
| | | | | | | | | | | | 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.
* gnu: r-topgo: Update to 2.38.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
* gnu: r-summarizedexperiment: Update to 1.16.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
* gnu: r-delayedarray: Update to 0.12.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
* gnu: r-biocparallel: Update to 1.20.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
* gnu: r-shortread: Update to 1.44.1.Ricardo Wurmus2019-12-27
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
* gnu: python-bbknn: Update to 1.3.6.Brett Gilio2019-12-23
| | | | | | | * 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.
* gnu: tophat: Build with GCC 5Mădălin Ionel Patrașcu2019-12-23
| | | | | | | | * 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>
* gnu: fastx-toolkit: Build with GCC 6Mădălin Ionel Patrașcu2019-12-21
| | | | | | * gnu/packages/bioinformatics.scm (fastx-toolkit)[native-inputs]: Add gcc-6. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: r-scater: Update to 1.14.6.Ricardo Wurmus2019-12-20
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
* gnu: Add libsbml.Ricardo Wurmus2019-12-17
| | | | * gnu/packages/bioinformatics.scm (libsbml): New variable.
* gnu: r-seurat: Update to 3.1.2.Ricardo Wurmus2019-12-17
| | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
* gnu: python-gffutils: Update description.Ricardo Wurmus2019-12-16
| | | | | * gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow paragraph and fix spelling of SQLite.
* gnu: Add python-gffutils.Mădălin Ionel Patrașcu2019-12-16
| | | | | | * gnu/packages/bioinformatics.scm (python-gffutils): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: python-pyfaidx: Update to 0.5.7.Mădălin Ionel Patrașcu2019-12-16
| | | | * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
* gnu: r-genefilter: Update to 1.68.0.Ricardo Wurmus2019-12-15
| | | | | * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0. [propagated-inputs]: Remove r-s4vectors and add r-biocgenerics.
* gnu: r-deseq2: Update to 1.26.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
* gnu: r-dexseq: Update to 1.32.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
* gnu: r-annotationforge: Update to 1.28.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
* gnu: r-rbgl: Update to 1.62.1.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
* gnu: r-gseabase: Update to 1.48.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
* gnu: r-category: Update to 2.52.1.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
* gnu: r-gostats: Update to 2.52.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
* gnu: r-shortread: Update to 1.44.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0.
* gnu: r-systempiper: Update to 1.20.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0.
* gnu: r-grohmm: Update to 1.20.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.20.0.
* gnu: r-biocviews: Update to 1.54.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.54.0.
* gnu: r-biocstyle: Update to 2.14.2.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.2.
* gnu: r-bioccheck: Update to 1.22.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.22.0.
* gnu: r-s4vectors: Update to 0.24.1.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.1.
* gnu: r-iranges: Update to 2.20.1.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.1.
* gnu: r-genomeinfodb: Update to 1.22.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.0.
* gnu: r-edger: Update to 3.28.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.0.
* gnu: r-variantannotation: Update to 1.32.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.32.0.
* gnu: r-limma: Update to 3.42.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.0.
* gnu: r-xvector: Update to 0.26.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.26.0.
* gnu: r-genomicranges: Update to 1.38.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.38.0.
* gnu: r-biobase: Update to 2.46.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.46.0.
* gnu: r-annotationdbi: Update to 1.48.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.48.0.
* gnu: r-biomart: Update to 2.42.0.Ricardo Wurmus2019-12-15
| | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.0. [propagated-inputs]: Add r-biocfilecache, r-openssl, and r-rappdirs; remove r-rcurl.
* gnu: r-biocparallel: Update to 1.20.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.0.
* gnu: r-biostrings: Update to 2.54.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.54.0.
* gnu: r-rsamtools: Update to 2.2.1.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.1.
* gnu: r-delayedarray: Update to 0.12.0.Ricardo Wurmus2019-12-15
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.0.
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