| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
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This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through
8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5.
Specifically, these commits caused the build failure of
guix-package-cache.drv like this:
------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
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* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
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* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
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* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
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* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
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* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
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* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
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* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
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* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
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* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
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* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
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* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
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* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
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* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
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* gnu/packages/bioinformatics.scm (instrain): New variable.
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* gnu/packages/bioinformatics.scm (python-drep): New variable.
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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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