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2022-05-02gnu: htslib-for-stringtie: Inherit from htslib-1.12....* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from htslib-1.12. Ricardo Wurmus
2022-05-02gnu: python-cooler: Use more recent cytoolz....* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz-for-cooler with python-cytoolz. Ricardo Wurmus
2022-04-26gnu: Add r-giotto....* gnu/packages/bioinformatics.scm (r-giotto): New variable. Ricardo Wurmus
2022-04-19gnu: vcflib: Update to 1.0.3....* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3. [source]: Remove trailing #t. [arguments]: Remove trailing #t from phases. Efraim Flashner
2022-04-14gnu: scregseg: Remove cythonized file....* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file. Efraim Flashner
2022-04-14gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics)....* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here. Ricardo Wurmus
2022-04-11gnu: Add r-copykat....* gnu/packages/bioinformatics.scm (r-copykat): New variable. zimoun
2022-04-10gnu: smithwaterman: Fix cross-compiling....The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences. * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More closely match the 'ar' and 'ld' commands when substituting them. Efraim Flashner
2022-04-06gnu: Add r-rnaseqdtu....* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Hong Li
2022-04-05gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR....This is needed since the update of python-loompy. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename 'set-PYTHONPATH to 'set-additional-environment-variables and set NUMBA_CACHE_DIR. Ricardo Wurmus
2022-04-05gnu: pigx-scrnaseq: Use new inputs style....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list. Ricardo Wurmus
2022-04-05gnu: pigx-scrnaseq: Update to 1.1.8....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8. [patches]: Remove. [native-inputs]: Remove. * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2022-04-04gnu: freebayes: Fix test suite....* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python. Efraim Flashner
2022-04-04gnu: smithwaterman: Use new style for phases....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list of G-Expressions. Efraim Flashner
2022-04-04gnu: smithwaterman: Fix cross-compiling....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add make-flag to use cxx-for-target. Adjust custom 'patch-source and 'build-dynamic phases to use cross toolchain binaries when cross compiling. Remove trailing #t from phases. Efraim Flashner
2022-03-31gnu: python-velocyto: Set cache directory for Numba....* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir. Ricardo Wurmus
2022-03-31gnu: wfmash: Enable test suite....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools. Efraim Flashner
2022-03-31gnu: Add wfmash....* gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: htslib: Add bzip2 and xz to inputs....htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner <efraim@flashner.co.il> Arun Isaac
2022-03-31gnu: python-loompy: Update to 3.0.7....* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7. [arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir; respect TESTS? argument in 'check phase. [propagated-inputs]: Add python-click, python-numba, and python-numpy-groupies. Ricardo Wurmus
2022-03-29gnu: r-signac: Update to 1.6.0-2.458e647....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647. [propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings, r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-03-29gnu: plink-ng: Update to 2.00a3-20220315....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315. Ricardo Wurmus
2022-03-29gnu: Add r-cytobackbone....* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-03-29gnu: pigx-sars-cov2-ww: Update to 0.0.5....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5. [source]: Remove patch. [arguments]: Disable tests. * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2022-03-29gnu: pigx-rnaseq: Update to 0.0.20....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20. [source]: Remove patch. [inputs]: Add megadepth. * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2022-03-09gnu: Add r-scopeloomr....* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable. Ricardo Wurmus
2022-03-02gnu: texlive-latex-pgf: Rename to "texlive-pgf"....Suggested by Ricardo Wurmus. * gnu/packages/tex.scm (texlive-latex-pgf): Rename to... (texlive-pgf): ... this. Change 'name' accordingly. (texlive-latex-pgf): Define as deprecated. (texlive-beamer)[propagated-inputs]: Use the new name. (texlive-todonotes)[propagated-inputs]: Likewise. (texlive-adjustbox)[propagated-inputs]: Likewise. (texlive-tcolorbox)[propagated-inputs]: Likewise. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise. Ludovic Courtès
2022-02-27gnu: minimap2: Update to 2.24....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24. Efraim Flashner
2022-02-22gnu: Add r-dyngen....* gnu/packages/bioinformatics.scm (r-dyngen): New variable. Ricardo Wurmus
2022-02-15gnu: python-gffutils: Update to 0.10.1....* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it. Marius Bakke
2022-01-31gnu: Add scvelo....* gnu/packages/bioinformatics.scm (scvelo): New variable. Ricardo Wurmus
2022-01-31gnu: python-louvain-0.6: Update to 0.7.1....* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1. [arguments]: Add build phases 'find-igraph and 'pretend-version. [native-inputs]: Add python-setuptools-scm and python-wheel. Rename this variable... (python-louvain-0.7): ...to this, naturally. * gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update reference to python-louvain-0.6. Ricardo Wurmus
2022-01-31gnu: bwa-meth: Remove trailing #T from build phase....* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase. Ricardo Wurmus
2022-01-31gnu: bwa-meth: Update to 0.2.3....* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3. Ricardo Wurmus
2022-01-27gnu: pigx-sars-cov2-ww: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set PYTHONPATH variable in new build phase. Ricardo Wurmus
2022-01-27gnu: pigx-scrnaseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH variable in new build phase. Ricardo Wurmus
2022-01-27gnu: pigx-bsseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH variable in new build phase. Ricardo Wurmus
2022-01-27gnu: pigx-chipseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH variable in new build phase. Ricardo Wurmus
2022-01-27gnu: pigx-rnaseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH. * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH variable in new build phase. Ricardo Wurmus
2022-01-22gnu: cwltool: Update to 3.1.20220119140128....* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128. [propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB. [native-inputs]: Remove PYTHON-RDFLIB-JSONLD. Marius Bakke
2022-01-22gnu: python-pyvcf: Build with old setuptools....* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add PYTHON-SETUPTOOLS. Marius Bakke
2022-01-21gnu: Add r-scseqcomm....* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable. zimoun
2022-01-21gnu: Add r-icellnet....* gnu/packages/bioinformatics.scm (r-icellnet): New variable. zimoun
2022-01-20gnu: samtools-0.1: Install headers and library....* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases 'install-library and 'install-headers. Ricardo Wurmus
2022-01-20gnu: Add r-doubletfinder....* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable. Ricardo Wurmus
2022-01-18gnu: python-rdflib: Update to 6.1.1....* gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1. [arguments]: Remove #:tests. Add #:phases. [native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST. (python-rdflib-5): New variable. (python2-rdflib): Inherit from PYTHON-RDFLIB-5. * gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to PYTHON-RDFLIB-5. * gnu/packages/bioinformatics.scm (cwltool): Likewise. Marius Bakke
2022-01-17Merge branch 'version-1.4.0'...With resolved conflicts in: gnu/packages/gnome.scm gnu/packages/openstack.scm gnu/packages/python-xyz.scm Maxim Cournoyer
2022-01-17gnu: sambamba: Update to 0.8.2....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2. [arguments]: Sett CC and D_LD in build phase. [native-inputs]: Add ld-gold-wrapper and binutils-gold. Ricardo Wurmus
2022-01-10gnu: clipper: Remove obsolete phase....* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Sarah Morgensen
2022-01-10gnu: python-biom-format: Remove obsolete phase....* gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Sarah Morgensen
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