summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
Commit message (Collapse)AuthorAge
* 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
|\
| * 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.
* | gnu: taxtastic: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
* | gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
* | gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
* | gnu: phylip: Update to 3.697.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
* | gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
* | gnu: phylip: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
* | gnu: subread: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
* | gnu: subread: Update to 2.0.3.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
* | gnu: subread: Update home page..Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
* | gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | | | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-23 11:14:37 +0000