| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
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* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
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* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
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* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
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* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
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* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
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* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
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* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
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* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
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* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
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* gnu/packages/bioinformatics.scm (bandage): New variable.
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* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
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* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
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* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
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* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
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* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
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* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
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* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
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* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
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This is a follow-up to commit f1f6e49190a11f926af3bef0d45541cabf47c742.
* gnu/packages/bioinformatics.scm (star-for-pigx): New variable.
(pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
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* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
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* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
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* gnu/packages/bioinformatics.scm (prinseq): New variable.
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* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
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* gnu/packages/bioinformatics.scm (r-archr): New variable.
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* gnu/packages/bioinformatics.scm (indelfixer): New variable.
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* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0.
[arguments]: Set CC in make flags.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
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* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
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* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
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* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
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* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
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* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
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This package depends on Python 2 and doesn't build anymore. Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6.
* gnu/packages/bioinformatics.scm (grocsvs): Delete.
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* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
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* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
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* gnu/packages/bioinformatics.scm (trf): New variable.
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* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
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* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove
vcflib-source, intervaltree-source. Move vcflib ...
[inputs]: ... to here.
[arguments]: Adjust 'patch-source and 'unpack-submodule-sources for
changes in vendored code.
* gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
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