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2022-06-16gnu: Add pyscenic....* gnu/packages/bioinformatics.scm (pyscenic): New variable. Ricardo Wurmus
2022-06-16gnu: Add python-arboreto....* gnu/packages/bioinformatics.scm (python-arboreto): New variable. Ricardo Wurmus
2022-06-16gnu: Add python-ctxcore....* gnu/packages/bioinformatics.scm (python-ctxcore): New variable. Ricardo Wurmus
2022-06-09gnu: python-pybedtools: Update to 0.9.0....* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.9.0. [description]: Update to satisfy guix lint. [license]: Update to expat and lgpl2.1+. Vagrant Cascadian
2022-06-06gnu: discrover: Use reproducible timestamps....* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add 'set-force-source-date phase. Vagrant Cascadian
2022-06-01gnu: pigx-scrnaseq: Update to 1.1.9....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.9. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. Ricardo Wurmus
2022-06-01gnu: pigx-bsseq: Update to 0.1.7....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.7. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove automake and autoconf. * gnu/packages/patches/pigx-bsseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus
2022-06-01gnu: pigx-chipseq: Update to 0.1.0....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.1.0. [source]: Remove patch. [arguments]: Remove 'autoreconf phase. [native-inputs]: Remove autoconf and automake. * gnu/packages/patches/pigx-chipseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove patch. Ricardo Wurmus
2022-06-01gnu: pigx-rnaseq: Update to 0.1.0....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.0. [arguments]: Remove phase 'patch-knitr. Ricardo Wurmus
2022-06-01gnu: pigx-rnaseq: Update to 0.0.21....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.21. Ricardo Wurmus
2022-06-01gnu: pigx-rnaseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'patch-knitr. Ricardo Wurmus
2022-06-01gnu: Add sylamer....* gnu/packages/bioinformatics.scm (sylamer): New variable. Ricardo Wurmus
2022-05-31gnu: Remove python2-biopython....* gnu/packages/bioinformatics.scm (python2-biopython): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove pplacer-scripts....* gnu/packages/bioinformatics.scm (pplacer-scripts): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove pplacer....* gnu/packages/bioinformatics.scm (pplacer): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-checkm-genome....* gnu/packages/bioinformatics.scm (python2-checkm-genome): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove fraggenescan....* gnu/packages/bioinformatics.scm (fraggenescan): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-pysam....* gnu/packages/bioinformatics.scm (python2-pysam): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove find-circ....* gnu/packages/bioinformatics.scm (find-circ): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove gess....* gnu/packages/bioinformatics.scm (gess): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove pyicoteo....* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-pbcore....* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-pyfaidx....* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-screed....* gnu/packages/bioinformatics.scm (python2-screed): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove miso....* gnu/packages/bioinformatics.scm (miso): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-warpedlmm....* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove poretools....* gnu/packages/bioinformatics.scm (poretools): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-dendropy....* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove bamm....* gnu/packages/bioinformatics.scm (bamm): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-pybedtools....* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-htseq....* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove pepr....* gnu/packages/bioinformatics.scm (pepr): Delete variable. Maxim Cournoyer
2022-05-31gnu: tetoolkit: Update to 2.2.1b....* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.1b. [python]: Delete argument. [phases]: Delete trailing #t. {make-writable}: Delete phase. {adjust-requirements}: New phase. {patch-invocations}: Use search-input-file. {wrap-program}: Use search-input-file. [inputs]: Remove python2-argparse. Replace python2-pysam with python-pysam. [home-page]: Update URL. Maxim Cournoyer
2022-05-31gnu: Remove python2-pybigwig....* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove ribodiff....* gnu/packages/bioinformatics.scm (ribodiff): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove grit....* gnu/packages/bioinformatics.scm (grit): Delete variable. Maxim Cournoyer
2022-05-31gnu: Remove python2-fastalite....* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable. Maxim Cournoyer
2022-05-30gnu: python-scanpy: Update to 1.9.1....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.1. [arguments]: Add phase 'set-numba-cache-dir; disable more broken tests. [propagated-inputs]: Add python-dask and python-session-info; replace python-louvain-0.7 with python-louvain. Ricardo Wurmus
2022-05-29gnu: pigx-sars-cov-2: Fix build....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add 'autoreconf phase to patch build system. Ricardo Wurmus
2022-05-29gnu: pigx-bsseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system in 'autoreconf phase. Ricardo Wurmus
2022-05-29gnu: pigx-scrnaseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Add autoreconf step to work around m4 macro bug and missing VERSION file. [native-inputs]: Add autoconf and automake. Ricardo Wurmus
2022-05-29gnu: pigx-chipseq: Fix build....* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build system. Ricardo Wurmus
2022-05-22gnu: Fix all this damn packages....* gnu/packages/bioinformatics.scm (r-icellnet)[description]: Fix ‘this packages’ typo. * gnu/packages/cran.scm (r-add2ggplot)[description]: Likewise. * gnu/packages/crates-io.scm (rust-const-oid-0.6, rust-pem-rfc7468-0.2) (rust-scrypt-0.8)[description]: Likewise. Tobias Geerinckx-Rice
2022-05-25Move (gnu platform) and (gnu platforms ...) to guix/....* gnu/platform.scm: * gnu/platforms/arm.scm: * gnu/platforms/hurd.scm: * gnu/platforms/mips.scm: * gnu/platforms/powerpc.scm: * gnu/platforms/riscv.scm: * gnu/platforms/s390.scm: * gnu/platforms/x86.scm: Move to guix/. * Makefile.am: * doc/guix.texi (Porting to a New Platform): * etc/release-manifest.scm: * gnu/ci.scm: * gnu/image.scm: * gnu/local.mk: * gnu/packages/bioinformatics.scm: * gnu/packages/bootstrap.scm: * gnu/packages/cross-base.scm: * gnu/packages/instrumentation.scm: * gnu/packages/linux.scm: * gnu/system/image.scm: * gnu/system/images/hurd.scm: * gnu/system/images/novena.scm: * gnu/system/images/pine64.scm: * gnu/system/images/pinebook-pro.scm: * gnu/system/images/rock64.scm: * guix/scripts/build.scm: * guix/scripts/system.scm: * guix/self.scm: Update (gnu platform...) to (guix platform...). Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Josselin Poiret
2022-05-22linux: Remove system->linux-architecture procedure....* 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. Mathieu Othacehe
2022-05-12gnu: fastahack: Wrap long line....* gnu/packages/bioinformatics.scm (fastahack): Wrap long line. Arun Isaac
2022-05-11gnu: cwltool: Do not propagate inputs....* gnu/packages/bioinformatics.scm (cwltool)[propagated-inputs]: Move to ... [inputs]: ... here. Arun Isaac
2022-05-09gnu: vcflib: Set absolute path to pkg-config....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> Arun Isaac
2022-05-09gnu: vcflib: Find submodule sources in native-inputs during cross-compilation....* 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> Arun Isaac
2022-05-09gnu: vcflib: Use G-expressions....* 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> Arun Isaac