Age | Commit message (Collapse) | Author |
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
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* 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.
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* gnu/packages/bioinformatics.scm (python-pyspoa)[synopsis]: Fix trailing
whitespace.
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* gnu/packages/bioinformatics.scm (lofreq)[synopsis]: Fix trailing whitespace.
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* gnu/packages/bioinformatics.scm (arriba)[synopsis]: Fix trailing whitespace.
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* gnu/packages/bioinformatics.scm (ivar)[description]: Fix trailing
whitespace.
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* 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.
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* 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.
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This commit was obtained by running:
./pre-inst-env guix style
without any additional argument.
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* gnu/packages/bioinformatics.scm (salmon): Update to 1.6.0.
[inputs]: Update pufferfish sources.
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* gnu/packages/bioinformatics.scm (ccwl): New variable.
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* gnu/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl with
gsl-static.
* gnu/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Same.
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* gnu/packages/bioinformatics.scm (python-dendropy)[arguments]: Adjust
custom 'skip-broken-tests phase to skip additional test.
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* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove cmake flag.
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* gnu/packages/bioinformatics.scm (repeat-masker): Update to 4.1.2-p1.
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* 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.
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* 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.
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* 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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* gnu/packages/bioinformatics.scm (samtools-1.2): New variable.
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* gnu/packages/bioinformatics.scm (htslib-for-samtools-1.2): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (paml)[arguments]: Set CFLAGS.
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* gnu/packages/bioinformatics.scm (paml)[arguments]: Remove trailing #T from
build phases.
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* gnu/packages/bioinformatics.scm (sambamba)[arguments]: Remove trailing #T
from build phases.
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* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add
texlive-fonts-ec.
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* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove trailing #T
from build phases.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test
suite.
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* gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
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* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T
from 'install phase.
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* gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS?
option.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
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* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
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* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from
build phase.
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* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
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* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
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* 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.
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* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
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* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
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* gnu/packages/bioinformatics.scm (pbcopper): New variable.
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* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6.
[arguments]: Remove trailing #T.
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* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all
generated .c files.
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* 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.
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