| Age | Commit message (Expand) | Author |
|---|
| 2022-01-10 | gnu: samtools: Update to 1.14....* 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.
| Maxim Cournoyer |
| 2022-01-10 | gnu: htslib: Update to 1.14....* 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.
| Maxim Cournoyer |
| 2022-01-11 | gnu: stringtie: Update to 2.2.0....* 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.
| Ricardo Wurmus |
| 2022-01-11 | gnu: Add htslib-for-stringtie....* 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.
| Ricardo Wurmus |
| 2022-01-04 | gnu: r-archr: Update to 1.0.1-1.92ab814....* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
| Ricardo Wurmus |
| 2021-12-30 | gnu: Remove trailing period from synopsis....* 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.
| Vagrant Cascadian |
| 2021-12-30 | gnu: python-pyspoa: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (python-pyspoa)[synopsis]: Fix trailing
whitespace.
| Vagrant Cascadian |
| 2021-12-30 | gnu: lofreq: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (lofreq)[synopsis]: Fix trailing whitespace.
| Vagrant Cascadian |
| 2021-12-30 | gnu: arriba: Fix trailing whitespace in synopsis....* gnu/packages/bioinformatics.scm (arriba)[synopsis]: Fix trailing whitespace.
| Vagrant Cascadian |
| 2021-12-29 | gnu: ivar: Fix trailing whitespace in description....* gnu/packages/bioinformatics.scm (ivar)[description]: Fix trailing
whitespace.
| Vagrant Cascadian |
| 2021-12-20 | gnu: sortmerna: Update to 4.3.4....* 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.
| Ricardo Wurmus |
| 2021-12-17 | gnu: Remove unneeded uses of custom GCC versions....* 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.
| Marius Bakke |
| 2021-12-13 | gnu: Simplify package inputs....This commit was obtained by running:
./pre-inst-env guix style
without any additional argument.
| Ludovic Courtès |
| 2021-12-12 | gnu: salmon: Update to 1.6.0....* gnu/packages/bioinformatics.scm (salmon): Update to 1.6.0.
[inputs]: Update pufferfish sources.
| Ricardo Wurmus |
| 2021-12-10 | Merge remote-tracking branch 'signed/master' into core-updates | Mathieu Othacehe |
| 2021-12-10 | gnu: Add ccwl....* gnu/packages/bioinformatics.scm (ccwl): New variable.
| Arun Isaac |
| 2021-12-09 | gnu: pplacer: Fix build....* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with
gsl-static.
* gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.
| Efraim Flashner |
| 2021-12-09 | gnu: python-dendropy: Skip additional test....* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.
| Efraim Flashner |
| 2021-12-09 | gnu: imp: Build with default cmake....* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
| Efraim Flashner |
| 2021-12-09 | gnu: repeat-masker: Update to 4.1.2-p1....* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
| Ricardo Wurmus |
| 2021-12-09 | gnu: metabat: Update to 2.15....* 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.
| Ricardo Wurmus |
| 2021-12-09 | gnu: seek: Update to 1-1.196ed4c....* 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.
| Ricardo Wurmus |
| 2021-12-09 | gnu: miso: Update to 0.5.4-1.b714021....* 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.
| Ricardo Wurmus |
| 2021-12-09 | gnu: Add samtools-1.2....* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
| Ricardo Wurmus |
| 2021-12-09 | gnu: Add htslib-for-samtools-1.2....* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
| Ricardo Wurmus |
| 2021-12-08 | gnu: tadbit: Update to 1.0.1-1.5c4c1dd....* 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.
| Ricardo Wurmus |
| 2021-12-08 | gnu: paml: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-08 | gnu: paml: Remove trailing #T....* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
| Ricardo Wurmus |
| 2021-12-08 | gnu: sambamba: Remove trailing #T....* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-08 | gnu: discrover: Add texlive-fonts-ec to inputs....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-fonts-ec.
| Ricardo Wurmus |
| 2021-12-08 | gnu: discrover: Remove trailing #T....* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-08 | gnu: tbsp: Update to 1.0.0-2.dc30c03....* 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.
| Ricardo Wurmus |
| 2021-12-08 | gnu: mantis: Update to 0.1-2.b6979a2....* 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.
| Ricardo Wurmus |
| 2021-12-08 | gnu: imp: Disable tests....* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
| Ricardo Wurmus |
| 2021-12-08 | gnu: snap-aligner: Update to 2.0.0....* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
| Ricardo Wurmus |
| 2021-12-08 | gnu: snap-aligner: Remove trailing #T....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T
from 'install phase.
| Ricardo Wurmus |
| 2021-12-08 | gnu: snap-aligner: Run tests conditionally....* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS?
option.
| Ricardo Wurmus |
| 2021-12-08 | gnu: khmer: Cythonize source files....* 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.
| Ricardo Wurmus |
| 2021-12-08 | gnu: cwltool: Update to 3.1.20211107152837....* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: newick-utils: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-07 | gnu: blasr: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
| Ricardo Wurmus |
| 2021-12-07 | gnu: blasr: Remove trailing #T....* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from
build phase.
| Ricardo Wurmus |
| 2021-12-07 | gnu: blasr-libcpp: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
| Ricardo Wurmus |
| 2021-12-07 | gnu: htseq: Update to 0.12.3....* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
| Ricardo Wurmus |
| 2021-12-07 | gnu: clipper: Update to 2.0.1....* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: pbbam: Update to 1.7.0....* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
| Ricardo Wurmus |
| 2021-12-07 | gnu: bwa-pssm: Fix build....* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Add pbcopper....* gnu/packages/bioinformatics.scm (pbcopper): New variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: fsom: Build with GCC 6....* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6.
[arguments]: Remove trailing #T.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-velocyto: Remove generated C files....* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all
generated .c files.
| Ricardo Wurmus |
