| Age | Commit message (Expand) | Author |
|---|
| 2022-01-31 | gnu: Add scvelo....* gnu/packages/bioinformatics.scm (scvelo): New variable.
| Ricardo Wurmus |
| 2022-01-31 | gnu: python-louvain-0.6: Update to 0.7.1....* 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.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Remove trailing #T from build phase....* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Update to 0.2.3....* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-sars-cov2-ww: Fix Python module capture....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.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-scrnaseq: Fix Python module capture....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.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-bsseq: Fix Python module capture....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.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-chipseq: Fix Python module capture....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.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-rnaseq: Fix Python module capture....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.
| Ricardo Wurmus |
| 2022-01-22 | gnu: cwltool: Update to 3.1.20220119140128....* 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.
| Marius Bakke |
| 2022-01-22 | gnu: python-pyvcf: Build with old setuptools....* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add
PYTHON-SETUPTOOLS.
| Marius Bakke |
| 2022-01-21 | gnu: Add r-scseqcomm....* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
| zimoun |
| 2022-01-21 | gnu: Add r-icellnet....* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
| zimoun |
| 2022-01-20 | gnu: samtools-0.1: Install headers and library....* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases
'install-library and 'install-headers.
| Ricardo Wurmus |
| 2022-01-20 | gnu: Add r-doubletfinder....* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
| Ricardo Wurmus |
| 2022-01-18 | gnu: python-rdflib: Update to 6.1.1....* 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.
| Marius Bakke |
| 2022-01-17 | Merge branch 'version-1.4.0'...With resolved conflicts in:
gnu/packages/gnome.scm
gnu/packages/openstack.scm
gnu/packages/python-xyz.scm
| Maxim Cournoyer |
| 2022-01-17 | gnu: sambamba: Update to 0.8.2....* 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.
| Ricardo Wurmus |
| 2022-01-10 | gnu: clipper: Remove obsolete phase....* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| Sarah Morgensen |
| 2022-01-10 | gnu: python-biom-format: Remove obsolete phase....* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| Sarah Morgensen |
| 2022-01-10 | gnu: python-pysam: Update to 0.18.0....* 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.
| Maxim Cournoyer |
| 2022-01-10 | gnu: bcftools: Update to 1.14....* 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.
| Maxim Cournoyer |
| 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 |
