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* 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.
* | gnu: Add samtools-1.2.Ricardo Wurmus2021-12-09
| | | | | | | | * gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
* | gnu: Add htslib-for-samtools-1.2.Ricardo Wurmus2021-12-09
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
* | gnu: tadbit: Update to 1.0.1-1.5c4c1dd.Ricardo Wurmus2021-12-08
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-1.5c4c1dd. [arguments]: Remove trailing #T from build phases; pass -fcommon to test binaries; run tests conditionally.
* | gnu: paml: Pass -fcommon to compiler.Ricardo Wurmus2021-12-08
| | | | | | | | * gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
* | gnu: paml: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from build phases.
* | gnu: sambamba: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T from build phases.
* | gnu: discrover: Add texlive-fonts-ec to inputs.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add texlive-fonts-ec.
* | gnu: discrover: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T from build phases.
* | gnu: tbsp: Update to 1.0.0-2.dc30c03.Ricardo Wurmus2021-12-08
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03. [arguments]: Relax requirement on matplot. This may turn out to be a mistake. [inputs]: Replace python-biopython with python-biopython-1.73.
* | gnu: mantis: Update to 0.1-2.b6979a2.Ricardo Wurmus2021-12-08
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2. [arguments]: Disable the use of SSE4.2 instructions. [native-inputs]: Build with GCC 7.
* | gnu: imp: Disable tests.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite.
* | gnu: snap-aligner: Update to 2.0.0.Ricardo Wurmus2021-12-08
| | | | | | | | * gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
* | gnu: snap-aligner: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase.
* | gnu: snap-aligner: Run tests conditionally.Ricardo Wurmus2021-12-08
| | | | | | | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option.
* | gnu: khmer: Cythonize source files.Ricardo Wurmus2021-12-08
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files. [arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp files from Cython sources; add 'build-extensions phase; replace 'check phase.
* | gnu: cwltool: Update to 3.1.20211107152837.Ricardo Wurmus2021-12-08
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837. [arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T from build phases; fix /bin/sh invocations in test files.
* | gnu: newick-utils: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
* | gnu: blasr: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
* | gnu: blasr: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase.
* | gnu: blasr-libcpp: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib.
* | gnu: htseq: Update to 0.12.3.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
* | gnu: clipper: Update to 2.0.1.Ricardo Wurmus2021-12-07
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1. [source]: Add snippet to remove pre-compiled files. [arguments]: Disable tests, delete 'sanity-check phase, and add 'use-python3-for-cython phase.
* | gnu: pbbam: Update to 1.7.0.Ricardo Wurmus2021-12-07
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper.
* | gnu: bwa-pssm: Fix build.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error.
* | gnu: Add pbcopper.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (pbcopper): New variable.
* | gnu: fsom: Build with GCC 6.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T.
* | gnu: python-velocyto: Remove generated C files.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files.
* | gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus2021-12-07
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black.
* | gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus2021-12-07
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
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