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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
2022-05-09gnu: fastahack: Use compiler specific to the build target....* 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> Arun Isaac
2022-05-09gnu: fastahack: Use G-expressions....* 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> Arun Isaac
2022-05-09gnu: tabixpp: Fix cross-compilation....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> Arun Isaac
2022-05-09gnu: tabixpp: Use build tools specific to the target....* 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> Arun Isaac
2022-05-09gnu: tabixpp: Use #:make-flags....* 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> Arun Isaac
2022-05-09gnu: tabixpp: Use G-expressions....* 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> Arun Isaac
2022-05-06gnu: pigx-sars-cov-2: Update to 0.0.7....* 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. Ricardo Wurmus
2022-05-06gnu: Add pigx-sars-cov-2....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): New variable. (pigx-sars-cov2-ww): Deprecate this package in favor of the former. Ricardo Wurmus
2022-05-02gnu: python-hic2cool: Fix build....* gnu/packages/bioinformatics.scm (python-hic2cool)[arguments]: Fix incompatibility with h5py 3; disable two tests. Ricardo Wurmus
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