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2022-05-31gnu: Remove find-circ.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (find-circ): Delete variable.
2022-05-31gnu: Remove gess.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (gess): Delete variable.
2022-05-31gnu: Remove pyicoteo.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pyicoteo): Delete variable.
2022-05-31gnu: Remove python2-pbcore.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pbcore): Delete variable.
2022-05-31gnu: Remove python2-pyfaidx.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pyfaidx): Delete variable.
2022-05-31gnu: Remove python2-screed.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-screed): Delete variable.
2022-05-31gnu: Remove miso.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (miso): Delete variable.
2022-05-31gnu: Remove python2-warpedlmm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-warpedlmm): Delete variable.
2022-05-31gnu: Remove poretools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (poretools): Delete variable.
2022-05-31gnu: Remove python2-dendropy.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-dendropy): Delete variable.
2022-05-31gnu: Remove bamm.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bamm): Delete variable.
2022-05-31gnu: Remove python2-pybedtools.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybedtools): Delete variable.
2022-05-31gnu: Remove python2-htseq.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-htseq): Delete variable.
2022-05-31gnu: Remove pepr.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (pepr): Delete variable.
2022-05-31gnu: tetoolkit: Update to 2.2.1b.Maxim Cournoyer
* 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.
2022-05-31gnu: Remove python2-pybigwig.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-pybigwig): Delete variable.
2022-05-31gnu: Remove ribodiff.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
2022-05-31gnu: Remove grit.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (grit): Delete variable.
2022-05-31gnu: Remove python2-fastalite.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (python2-fastalite): Delete variable.
2022-05-30gnu: python-scanpy: Update to 1.9.1.Ricardo Wurmus
* 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.
2022-05-29gnu: pigx-sars-cov-2: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[arguments]: Add 'autoreconf phase to patch build system.
2022-05-29gnu: pigx-bsseq: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Patch build system in 'autoreconf phase.
2022-05-29gnu: pigx-scrnaseq: Fix build.Ricardo Wurmus
* 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.
2022-05-29gnu: pigx-chipseq: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Patch build system.
2022-05-22gnu: Fix all this damn packages.Tobias Geerinckx-Rice
* 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.
2022-05-25Move (gnu platform) and (gnu platforms ...) to guix/.Josselin Poiret
* 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>
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>
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