| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2021-12-07 | gnu: python-schema-salad: Update to 8.2.20211116214159....* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: taxtastic: Update to 0.9.2....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust
'prepare-directory phase.
| Ricardo Wurmus |
| 2021-12-07 | gnu: taxtastic: Run tests conditionally....* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-dendropy: Update to 4.5.1....* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-cooler: Use python-cytoolz-for-cooler....* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Update to 3.697....* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Remove trailing #T....* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Remove trailing #T....* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Update to 2.0.3....* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Update home page.....* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
| Ricardo Wurmus |
