Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
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* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
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This is a follow-up to commit 239716fb0ba0a7cd81f9d59dcf5a2261b8efe4fa.
* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
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* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
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This fixes <https://bugs.gnu.org/32184>.
* gnu/packages/cups.scm (hplip)[source]: Add patch. Update snippet to
remove non-free code and binary blobs.
* gnu/packages/patches/hplip-remove-imageprocessor.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
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* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
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* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
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* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
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* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
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* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
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* gnu/packages/benchmark.scm (fio): Update to 3.11.
[source]: Use bz2 compressed tarball.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
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* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
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* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
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* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
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* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
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* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
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* gnu/packages/music.scm (clementine)[inputs]: Use sqlite-with-column-metadata.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
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* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
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* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
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* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
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* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
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* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
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* gnu/packages/ci.scm (cuirass): Update to 0b40dca.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
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* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
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* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
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* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
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* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
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