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2022-05-22linux: Remove system->linux-architecture procedure.Mathieu Othacehe
* gnu/packages/linux.scm (system->linux-architecture): Remove it. (make-linux-libre-headers*, make-linux-libre*): Adapt them. * guix/build-system/linux-module.scm (system->arch): Adapt it. * gnu/packages/instrumentation.scm (uftrace): Ditto. * gnu/packages/cross-base.scm (cross-kernel-headers): Ditto. * gnu/packages/bioinformatics.scm (ncbi-vdb): Ditto. * doc/guix.texi (Porting to a new platform): Update it.
2022-05-12gnu: fastahack: Wrap long line.Arun Isaac
* gnu/packages/bioinformatics.scm (fastahack): Wrap long line.
2022-05-11gnu: cwltool: Do not propagate inputs.Arun Isaac
* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ... [inputs]: ... here.
2022-05-09gnu: vcflib: Set absolute path to pkg-config.Arun Isaac
Setting the absolute path to pkg-config is required to support cross-compilation. * gnu/packages/bioinformatics.scm (vcflib)[arguments]: Set PKG_CONFIG_EXECUTABLE in #:configure-flags. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: vcflib: Find submodule sources in native-inputs during cross-compilation.Arun Isaac
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In the unpack-submodule-sources phase, look for submodule sources in both inputs and native-inputs. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: vcflib: Use G-expressions.Arun Isaac
* gnu/packages/bioinformatics.scm (vcflib)[source, arguments]: Rewrite using G-expressions. [arguments]: Do not return #t from custom phases. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: fastahack: Use compiler specific to the build target.Arun Isaac
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Set CXX in #:make-flags. In the build-dynamic phase, use cxx-for-target instead of g++. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: fastahack: Use G-expressions.Arun Isaac
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Rewrite using G-expressions. Do not return #t from custom phases. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: tabixpp: Fix cross-compilation.Arun Isaac
tabixpp 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 (tabixpp)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: tabixpp: Use build tools specific to the target.Arun Isaac
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Set CC and CXX in #:make-flags. In the build-libraries phase, use cxx-for-target instead of g++ and ar-for-target instead of ar. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: tabixpp: Use #:make-flags.Arun Isaac
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Do not override the build phase. Move the required make arguments to #:make-flags. Add build-libraries phase. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-09gnu: tabixpp: Use G-expressions.Arun Isaac
* gnu/packages/bioinformatics.scm (tabixpp)[source]: Reindent. [arguments]: Use search-input-file and search-input-directory. [source, arguments]: Rewrite using G-expressions. Do not return #t from snippets and custom phases. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-05-06gnu: pigx-sars-cov-2: Update to 0.0.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.7. [inputs]: Remove bbmap and prinseq; add r-viridis. [arguments]: Remove autoreconf phase.
2022-05-06gnu: Add pigx-sars-cov-2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable. (pigx-sars-cov2-ww): Deprecate this package in favor of the former.
2022-05-02gnu: python-hic2cool: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix incompatibility with h5py 3; disable two tests.
2022-05-02gnu: htslib-for-stringtie: Inherit from htslib-1.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-for-stringtie): Inherit from htslib-1.12.
2022-05-02gnu: python-cooler: Use more recent cytoolz.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz-for-cooler with python-cytoolz.
2022-04-26gnu: Add r-giotto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giotto): New variable.
2022-04-19gnu: vcflib: Update to 1.0.3.Efraim Flashner
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3. [source]: Remove trailing #t. [arguments]: Remove trailing #t from phases.
2022-04-14gnu: scregseg: Remove cythonized file.Efraim Flashner
* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file.
2022-04-14gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics).Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
2022-04-11gnu: Add r-copykat.zimoun
* gnu/packages/bioinformatics.scm (r-copykat): New variable.
2022-04-10gnu: smithwaterman: Fix cross-compiling.Efraim Flashner
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.
2022-04-06gnu: Add r-rnaseqdtu.Hong Li
* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-04-05gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR.Ricardo Wurmus
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.
2022-04-05gnu: pigx-scrnaseq: Use new inputs style.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
2022-04-05gnu: pigx-scrnaseq: Update to 1.1.8.Ricardo Wurmus
* 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.
2022-04-04gnu: freebayes: Fix test suite.Efraim Flashner
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
2022-04-04gnu: smithwaterman: Use new style for phases.Efraim Flashner
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list of G-Expressions.
2022-04-04gnu: smithwaterman: Fix cross-compiling.Efraim Flashner
* 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.
2022-03-31gnu: python-velocyto: Set cache directory for Numba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir.
2022-03-31gnu: wfmash: Enable test suite.Efraim Flashner
* 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.
2022-03-31gnu: Add wfmash.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2022-03-31gnu: htslib: Add bzip2 and xz to inputs.Arun Isaac
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>
2022-03-31gnu: python-loompy: Update to 3.0.7.Ricardo Wurmus
* 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.
2022-03-29gnu: r-signac: Update to 1.6.0-2.458e647.Mădălin Ionel Patrașcu
* 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>
2022-03-29gnu: plink-ng: Update to 2.00a3-20220315.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
2022-03-29gnu: Add r-cytobackbone.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-03-29gnu: pigx-sars-cov2-ww: Update to 0.0.5.Ricardo Wurmus
* 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.
2022-03-29gnu: pigx-rnaseq: Update to 0.0.20.Ricardo Wurmus
* 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.
2022-03-09gnu: Add r-scopeloomr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
2022-03-02gnu: texlive-latex-pgf: Rename to "texlive-pgf".Ludovic Courtès
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.
2022-02-27gnu: minimap2: Update to 2.24.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
2022-02-22gnu: Add r-dyngen.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
2022-02-15gnu: python-gffutils: Update to 0.10.1.Marius Bakke
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it.
2022-01-31gnu: Add scvelo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo): New variable.
2022-01-31gnu: python-louvain-0.6: Update to 0.7.1.Ricardo Wurmus
* 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.
2022-01-31gnu: bwa-meth: Remove trailing #T from build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase.
2022-01-31gnu: bwa-meth: Update to 0.2.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
2022-01-27gnu: pigx-sars-cov2-ww: Fix Python module capture.Ricardo Wurmus
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.
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