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* gnu: Add r-scopeloomr.Ricardo Wurmus2022-03-09
| | | | * gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
* gnu: texlive-latex-pgf: Rename to "texlive-pgf".Ludovic Courtès2022-03-02
| | | | | | | | | | | | | 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.
* gnu: minimap2: Update to 2.24.Efraim Flashner2022-02-27
| | | | * gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
* gnu: Add r-dyngen.Ricardo Wurmus2022-02-22
| | | | * gnu/packages/bioinformatics.scm (r-dyngen): New variable.
* gnu: python-gffutils: Update to 0.10.1.Marius Bakke2022-02-15
| | | | | | * gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it.
* gnu: Add scvelo.Ricardo Wurmus2022-01-31
| | | | * gnu/packages/bioinformatics.scm (scvelo): New variable.
* gnu: python-louvain-0.6: Update to 0.7.1.Ricardo Wurmus2022-01-31
| | | | | | | | | | * 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.
* gnu: bwa-meth: Remove trailing #T from build phase.Ricardo Wurmus2022-01-31
| | | | | * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T from build phase.
* gnu: bwa-meth: Update to 0.2.3.Ricardo Wurmus2022-01-31
| | | | * gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
* gnu: pigx-sars-cov2-ww: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | 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.
* gnu: pigx-scrnaseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | 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.
* gnu: pigx-bsseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | 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.
* gnu: pigx-chipseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | 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.
* gnu: pigx-rnaseq: Fix Python module capture.Ricardo Wurmus2022-01-27
| | | | | | | 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.
* gnu: cwltool: Update to 3.1.20220119140128.Marius Bakke2022-01-22
| | | | | | * 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.
* gnu: python-pyvcf: Build with old setuptools.Marius Bakke2022-01-22
| | | | | * gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add PYTHON-SETUPTOOLS.
* gnu: Add r-scseqcomm.zimoun2022-01-21
| | | | * gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
* gnu: Add r-icellnet.zimoun2022-01-21
| | | | * gnu/packages/bioinformatics.scm (r-icellnet): New variable.
* gnu: samtools-0.1: Install headers and library.Ricardo Wurmus2022-01-20
| | | | | * gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases 'install-library and 'install-headers.
* gnu: Add r-doubletfinder.Ricardo Wurmus2022-01-20
| | | | * gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
* gnu: python-rdflib: Update to 6.1.1.Marius Bakke2022-01-18
| | | | | | | | | | | * 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.
* Merge branch 'version-1.4.0'Maxim Cournoyer2022-01-17
|\ | | | | | | | | | | | | With resolved conflicts in: gnu/packages/gnome.scm gnu/packages/openstack.scm gnu/packages/python-xyz.scm
| * gnu: clipper: Remove obsolete phase.Sarah Morgensen2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| * gnu: python-biom-format: Remove obsolete phase.Sarah Morgensen2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format)[arguments] <#:phases>: Remove 'make-files-writable phase. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| * gnu: python-pysam: Update to 0.18.0.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0. [source]: Add FIXME to clarify bundled libraries in use. [phases]{check}: Streamline. [propagated-inputs]: Use latest htslib (1.14). [native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
| * gnu: bcftools: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.14. (bcftools-1.12): New variable. (bcftools-1.10): Use package/inherit and delete trailing #t. [name]: Delete field.
| * gnu: samtools: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.14. [modules]: Delete argument. [phases]{install-library, install-headers}: Delete phases. This version no longer includes the legacy library (it links to htslib directly). (samtools-1.12): New variable.
| * gnu: htslib: Update to 1.14.Maxim Cournoyer2022-01-10
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.14. (htslib-1.12): New variable. (htslib-1.10, htslib-1.9, htslib-1.3) (htslib-for-samtools-1.2): Normalize style.
* | gnu: sambamba: Update to 0.8.2.Ricardo Wurmus2022-01-17
| | | | | | | | | | | | * 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.
* | gnu: stringtie: Update to 2.2.0.Ricardo Wurmus2022-01-11
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0. [source]: Simplify snippet. [arguments]: Add make-flags; update build phases. [inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and libdeflate. [license]: Change to Expat license.
* | gnu: Add htslib-for-stringtie.Ricardo Wurmus2022-01-11
|/ | | | | | * gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable. * gnu/packages/patches/htslib-for-stringtie.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: r-archr: Update to 1.0.1-1.92ab814.Ricardo Wurmus2022-01-04
| | | | * gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
* gnu: Remove trailing period from synopsis.Vagrant Cascadian2021-12-30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/anddroid.scm (android-liblog, git-repo)[synopsis]: Remove trailing period. * gnu/packages/audio.scm (audio-to-midi)[synopsis]: Likewise. * gnu/packages/bioinformatics.scm (python-mygene, python-scanpy, nanosv)[synopsis]: Likewise. * gnu/packages/cran.scm (r-gsubfn)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-ascii-1, rust-bindgen-0.59, rust-byte-unit-4, rust-clircle-0.3, rust-dashmap-4, rust-dhcp4r-0.2, rust-fast-float-0.2, rust-fst-0.4, rust-futures-core-preview-0.3, rust-http-types-2, rust-hyper-0.14, rust-indexmap-1, rust-minimal-lexical-0.1, rust-oorandom-11.1, rust-runtime-raw-0.3, rust-sharded-slab-0.1, rust-takeable-option-0.4, rust-tower-service-0.3, rust-ttf-parser-0.12)[synopsis]: Likewise. * gnu/packages/disk.scm (f3)[synopsis]: Likewise. * gnu/packages/emacs-xyz.scm (emacs-scribble-mode, emacs-psession)[synopsis]: Likewise. * gnu/packages/golang.scm (go-github-com-kylelemons-godebug)[synopsis]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-fsnotify, ghc-libyaml, ghc-emojis, ghc-regex-tdfa, ghc-th-lift-instances, ghc-commonmark-pandoc)[synopsis]: Likewise. * gnu/packages/java.scm (java-commons-jxpath, java-jakarta-regexp)[synopsis]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-cl-annot, sbcl-envy)[synopsis]: Likewise. * gnu/packages/mail.scm (go-gitlab.com-shackra-goimapnotify)[synopsis]: Likewise. * gnu/packages/maven.scm (maven-wagon-http-shared, maven-surefire-plugin)[synopsis]: Likewise. * gnu/packages/perl.scm (perl-text-soundex)[synopsis]: Likewise. * gnu/packages/python-check.scm (python-httmock)[synopsis]: Likewise. * gnu/packages/python-web.scm (python-bottle)[synopsis]: Likewise. * gnu/packages/python-xyz.scm (python-olefile, python-tokenize-rt, python-pylzma)[synopsis]: Likewise. * gnu/packages/tex.scm (texlive-docstrip)[synopsis]: Likewise.
* gnu: python-pyspoa: Fix trailing whitespace in synopsis.Vagrant Cascadian2021-12-30
| | | | | * gnu/packages/bioinformatics.scm (python-pyspoa)[synopsis]: Fix trailing whitespace.
* gnu: lofreq: Fix trailing whitespace in synopsis.Vagrant Cascadian2021-12-30
| | | | * gnu/packages/bioinformatics.scm (lofreq)[synopsis]: Fix trailing whitespace.
* gnu: arriba: Fix trailing whitespace in synopsis.Vagrant Cascadian2021-12-30
| | | | * gnu/packages/bioinformatics.scm (arriba)[synopsis]: Fix trailing whitespace.
* gnu: ivar: Fix trailing whitespace in description.Vagrant Cascadian2021-12-29
| | | | | * gnu/packages/bioinformatics.scm (ivar)[description]: Fix trailing whitespace.
* gnu: sortmerna: Update to 4.3.4.Ricardo Wurmus2021-12-20
| | | | | | | | | * gnu/packages/bioinformatics.scm (sortmerna): Update to 4.3.4. [build-system]: Use cmake-build-system. [arguments]: Disable tests; add configure flags; add phase 'find-concurrentqueue-headers; update 'install phase. [inputs]: Add concurrentqueue, gflags, rapidjson, and rocksdb. [native-inputs]: Add pkg-config.
* gnu: Remove unneeded uses of custom GCC versions.Marius Bakke2021-12-17
| | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (libmaus2, biobambam2)[native-inputs]: Remove GCC-10. * gnu/packages/game-development.scm (libresprite, python-pyxel)[native-inputs]: Likewise. * gnu/packages/lua.scm (emilua)[native-inputs]: Likewise. * gnu/packages/radio.scm (sdr++)[native-inputs]: Likewise. * gnu/packages/wm.scm (fnott)[native-inputs]: Likewise. * gnu/packages/text-editors.scm (kakoune)[native-inputs]: Likewise. (scintilla)[native-inputs]: Remove GCC-9. * gnu/packages/build-tools.scm (bear)[native-inputs]: Likewise. * gnu/packages/cpp.scm (magic-enum)[native-inputs]: Likewise. * gnu/packages/games.scm (openttd)[native-inputs]: Likewise. (schiffbruch)[native-inputs]: Remove GCC-11. * gnu/packages/music.scm (liquidsfz, geonkick)[native-inputs]: Remove GCC-9. * gnu/packages/fcitx5.scm (fcitx5, libime, fcitx5-configtool)[native-inputs]: Likewise. * gnu/packages/wine.scm (dxvk32)[native-inputs]: Likewise. * gnu/packages/ftp.scm (libfilezilla)[native-inputs]: Remove GCC-8. * gnu/packages/image.scm (blurhash)[native-inputs]: Likewise. * gnu/packages/jami.scm (libring)[native-inputs]: Likewise. * gnu/packages/pdf.scm (xournalpp)[native-inputs]: Likewise. * gnu/packages/telegram.scm (webrtc-for-telegram-desktop, telegram-desktop)[native-inputs]: Likewise.
* gnu: Simplify package inputs.Ludovic Courtès2021-12-13
| | | | | | | | This commit was obtained by running: ./pre-inst-env guix style without any additional argument.
* gnu: salmon: Update to 1.6.0.Ricardo Wurmus2021-12-12
| | | | | * gnu/packages/bioinformatics.scm (salmon): Update to 1.6.0. [inputs]: Update pufferfish sources.
* Merge remote-tracking branch 'signed/master' into core-updatesMathieu Othacehe2021-12-10
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| * gnu: Add ccwl.Arun Isaac2021-12-10
| | | | | | | | * gnu/packages/bioinformatics.scm (ccwl): New variable.
* | gnu: pplacer: Fix build.Efraim Flashner2021-12-09
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with gsl-static. * gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.
* | gnu: python-dendropy: Skip additional test.Efraim Flashner2021-12-09
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust custom 'skip-broken-tests phase to skip additional test.
* | gnu: imp: Build with default cmake.Efraim Flashner2021-12-09
| | | | | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
* | gnu: repeat-masker: Update to 4.1.2-p1.Ricardo Wurmus2021-12-09
| | | | | | | | * gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
* | gnu: metabat: Update to 2.15.Ricardo Wurmus2021-12-09
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.15. [source]: Remove patch. [build-system]: Use cmake-build-system. [arguments]: Adjust to new build system. * gnu/packages/patches/metabat-fix-compilation.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* | gnu: seek: Update to 1-1.196ed4c.Ricardo Wurmus2021-12-09
| | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (seek): Update to 1-1.196ed4c. [source]: Fetch from github. [build-system]: Use cmake-build-system. [arguments]: Remove all custom phases; replace 'check phase; disable tests; set configure flags. [inputs]: Add apache-thrift:include, apache-thrift:lib, and python. [native-inputs]: Remove autoconf, automake, and perl; add pkg-config.
* | gnu: miso: Update to 0.5.4-1.b714021.Ricardo Wurmus2021-12-09
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (miso): Update to 0.5.4-1.b714021. [source]: Fetch via git; simplify snippet. [inputs]: Replace samtools with samtools-1.2. [home-page]: Update to new location.
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