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2021-01-14gnu: gemma: Add Texinfo markup....* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo markup. Efraim Flashner
2021-01-14gnu: gemma: Update to 0.98.3....* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3. [source, home-page]: Update to new upstream URI. [inputs]: Remove eigen, gfortran, lapack. [arguments]: Remove make-flags. Remove 'find-eigen phase. Rename 'bin-mkdir phase to 'prepare-build and substitute openblas include directory. Efraim Flashner
2020-12-29gnu: r-ggbio: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-ggbio): Move from here... * gnu/packages/bioconductor.scm (r-ggbio): ...to here. zimoun
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here. zimoun
2020-12-29gnu: r-snpstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-snpstats): Move from here... * gnu/packages/bioconductor.scm (r-snpstats): ...to here. zimoun
2020-12-29gnu: r-homo-sapiens: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here... * gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here. Replace 'string-append' by 'bioconductor-uri' with 'annotation'. zimoun
2020-12-29gnu: r-erma: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-erma): Move from here... * gnu/packages/bioconductor.scm (r-erma): ...to here. zimoun
2020-12-29gnu: r-ldblock: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-ldblock): Move from here... * gnu/packages/bioconductor.scm (r-ldblock): ...to here. zimoun
2020-12-29gnu: r-gqtlstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here... * gnu/packages/bioconductor.scm (r-gqtlstats): ...to here. zimoun
2020-12-29gnu: r-gviz: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gviz): Move from here... * gnu/packages/bioconductor.scm (r-gviz): ...to here. zimoun
2020-12-29gnu: r-gwascat: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-gwascat): Move from here... * gnu/packages/bioconductor.scm (r-gwascat): ...to here. zimoun
2020-12-29gnu: r-sushi: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-sushi): Move from here... * gnu/packages/bioconductor.scm (r-sushi): ...to here. zimoun
2020-12-20gnu: kentutils: Build with OpenSSL 1.1....* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0 to OPENSSL. Marius Bakke
2020-12-20gnu: kentutils: Add a file name for the "samtabix" input....* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix", add a file name on the origin. Marius Bakke
2020-12-09gnu: r-keggrest: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1. Ricardo Wurmus
2020-12-09gnu: r-genomeinfodb: Update to 1.26.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2. Ricardo Wurmus
2020-12-09gnu: r-biocstyle: Update to 2.18.1....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1. Ricardo Wurmus
2020-12-09gnu: r-rhtslib: Propagate zlib....* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here... [propagated-inputs]: ...to here. (r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5, r-methylkit)[inputs]: Remove zlib. * gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow, r-flowworkspace, r-seqbias)[inputs]: Remove zlib. Ricardo Wurmus
2020-12-09gnu: r-gqtlstats: Update to 1.21.3....* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3. zimoun
2020-12-09gnu: r-gqtlbase: Update to 1.21.1....Co-authored-by: Ricardo Wurmus <rekado@elephly.net> * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1. [arguments]: Add phase to patch broken NAMESPACE file. zimoun
2020-12-09gnu: r-biocviews: Update to 1.58.1....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1. Co-authored-by: Ricardo Wurmus <reka@elephly.net>. zimoun
2020-12-09gnu: r-rhdf5: Update to 2.34.0....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0. [propagated-inputs]: Add r-rhdf5filters. [arguments]: Avoid to have a plain directory on the list of libraries to link. Co-authored-by: Ricardo Wurmus <reka@elephly.net>. zimoun
2020-12-09gnu: Add r-rhdf5filters....* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable. Ricardo Wurmus
2020-12-09gnu: r-genomationdata: Update to 1.22.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0. zimoun
2020-12-09gnu: r-sushi: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0. zimoun
2020-12-09gnu: r-gwascat: Update to 2.22.0....* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0. [propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and r-rtracklayer. zimoun
2020-12-09gnu: r-gviz: Update to 1.34.0....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0. zimoun
2020-12-09gnu: r-ldblock: Update to 1.20.0....* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0. zimoun
2020-12-09gnu: r-erma: Update to 1.6.0....* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0. zimoun
2020-12-09gnu: r-snpstats: Update to 1.40.0....* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0. zimoun
2020-12-09gnu: r-ggbio: Update to 1.38.0....* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0. zimoun
2020-12-09gnu: r-biovizbase: Update to 1.38.0....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0. zimoun
2020-12-09gnu: r-organismdbi: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0. zimoun
2020-12-09gnu: r-ensembldb: Update to 2.14.0....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0. zimoun
2020-12-09gnu: r-dirichletmultinomial: Update to 1.32.0....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0. zimoun
2020-12-09gnu: r-complexheatmap: Update to 2.6.2....* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2; [propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and r-s4vectors. Roel Janssen
2020-12-09gnu: r-genomicfiles: Update to 1.26.0....* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0. [propagated-inputs]: Add r-matrixgenerics. zimoun
2020-12-09gnu: r-gage: Update to 2.40.0....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0. zimoun
2020-12-09gnu: r-keggrest: Update to 1.30.0....* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0. zimoun
2020-12-09gnu: r-fastseg: Update to 1.36.0....* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0. zimoun
2020-12-09gnu: r-annotationhub: Update to 2.22.0....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0. zimoun
2020-12-09gnu: r-interactivedisplaybase: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0. zimoun
2020-12-09gnu: r-edaseq: Update to 2.24.0....* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0. zimoun
2020-12-09gnu: r-aroma-light: Update to 3.20.0....* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0. zimoun
2020-12-09gnu: r-msnid: Update to 1.24.0....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0. [propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics, r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit, r-stringr, r-tibble, and r-xtable. zimoun
2020-12-09gnu: r-pcamethods: Update to 1.82.0....* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0. zimoun
2020-12-09gnu: r-mzid: Update to 1.28.0....* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0. [propagated-inputs]: Remove r-rcpp. zimoun
2020-12-09gnu: r-vsn: Update to 3.58.0....* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0. zimoun
2020-12-09gnu: r-affy: Update to 1.68.0....* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0. zimoun
2020-12-09gnu: r-affyio: Update to 1.60.0....* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0. zimoun