| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| ... | |
| * | gnu: python-dendropy: Update to 4.4.0.•••* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy):
Update to 4.4.0.
[source]: Use GitHub URI. Remove patch.
[properties]: Remove field.
(python2-dendropy)[arguments]: Run tests with setup.py.
[native-inputs]: Remove 'python2-nose.
* gnu/packages/patches/python-dendropy-fix-tests.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Delete it.
| Ben Woodcroft | 2018-07-29 | 1 | -19/+9 |
| * | gnu: Add python-fastalite.•••* gnu/packages/bioinformatics.scm (python-fastalite, python2-fastalite):
New variables.
| Ben Woodcroft | 2018-07-29 | 1 | -0/+23 |
| * | gnu: pigx-scrnaseq: Disable another expensive test.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Disable multiqc
test.
| Ricardo Wurmus | 2018-07-27 | 1 | -0/+1 |
| * | gnu: Add snakemake-4.•••* gnu/packages/python.scm (snakemake-4): New variable.
* gnu/packages/bioinformatics.scm (pigx-bsseq, pigx-rnaseq, pigx-scrnaseq,
pigx-chipseq)[inputs]: Use it.
| Ricardo Wurmus | 2018-07-27 | 1 | -4/+4 |
| * | gnu: java-picard: Fix manifest.•••* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Adjust phase
'edit-classpath-in-manifest for the new manifest generation code.
| Gábor Boskovits | 2018-07-26 | 1 | -1/+6 |
| * | gnu: macs: Update to 2.1.1.20160309.•••* gnu/packages/bioinformatics.scm (macs): Update to 2.1.1.20160309.
| Ricardo Wurmus | 2018-07-09 | 1 | -2/+2 |
| * | gnu: pigx: Update to 0.0.3.•••* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.3.
| Ricardo Wurmus | 2018-07-05 | 1 | -2/+2 |
| * | gnu: r-getopt: Move from bioinformatics to cran.•••* gnu/packages/bioinformatics.scm (r-getopt): Move from here...
* gnu/packages/cran.scm (r-getopt): ...to here.
| Ricardo Wurmus | 2018-07-05 | 1 | -22/+0 |
| * | gnu: pigx-scrnaseq: Update to 0.0.6.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.6.
[arguments]: Remove "wrap-executable" phase.
| Ricardo Wurmus | 2018-07-05 | 1 | -13/+3 |
| * | gnu: Add r-loomr.•••* gnu/packages/bioinformatics.scm (r-loomr): New variable.
| Ricardo Wurmus | 2018-07-03 | 1 | -0/+29 |
| * | gnu: pigx-bsseq: Update to 0.0.10.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.10.
[arguments]: Remove "wrap-executable" phase.
| Ricardo Wurmus | 2018-07-03 | 1 | -10/+2 |
| * | gnu: pigx-rnaseq: Update to 0.0.4.•••* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.4.
[arguments]: Remove "wrap-executable" phase.
| Ricardo Wurmus | 2018-07-03 | 1 | -10/+2 |
| * | gnu: pigx-chipseq: Update to 0.0.20.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.20.
| Ricardo Wurmus | 2018-07-03 | 1 | -2/+2 |
| * | gnu: Use more HTTPS.•••* gnu/packages/admin.scm (net-base, wakelan, pam-krb5)
[home-page]: Use HTTPS.
(dfc, libpcap, tcpdump, wpa-supplicant-minimal, libcap-ng, audit)
[source, home-page]: Likewise.
* gnu/packages/algebra.scm (eigen)[home-page]: Likewise.
(gp2c, pari-gp)[source, home-page]: Likewise.
* gnu/packages/animation.scm (etl, synfig, synfigstudio, papagayo)
[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (tadbit)[home-page]: Likewise.
| Tobias Geerinckx-Rice | 2018-06-22 | 1 | -1/+1 |
| * | gnu: pigx-chipseq: Update to 0.0.17.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.17.
[arguments]: Remove "wrap-executable" phase.
| Ricardo Wurmus | 2018-06-22 | 1 | -14/+4 |
| * | Do not record store file name in bioinformatics.scm.•••* gnu/packages/bioinformatics.scm (dropseq-tools): Replace full store
file name with ellipses.
| Ludovic Courtès | 2018-06-22 | 1 | -1/+1 |
| * | gnu: r-complexheatmap: Update to 1.18.1.•••* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.1.
| Ricardo Wurmus | 2018-06-21 | 1 | -2/+2 |
| * | gnu: r-delayedarray: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.1.
| Ricardo Wurmus | 2018-06-21 | 1 | -2/+2 |
| * | gnu: r-optparse: Update to 1.6.0.•••* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.0.
| Ricardo Wurmus | 2018-06-21 | 1 | -2/+2 |
| * | gnu: r-biocviews: Update to 1.48.2.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.2.
| Ricardo Wurmus | 2018-06-21 | 1 | -2/+2 |
| * | gnu: pigx-chipseq: Update to 0.0.16.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.16.
| Ricardo Wurmus | 2018-06-16 | 1 | -2/+2 |
| * | gnu: Add minimap2.•••* gnu/packages/bioinformatics.scm (minimap2): New variable.
| Ricardo Wurmus | 2018-06-14 | 1 | -0/+59 |
| * | gnu: pigx-bsseq: Update to 0.0.9.•••* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.9.
| Ricardo Wurmus | 2018-06-14 | 1 | -2/+2 |
| * | gnu: pigx-scrnaseq: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.5.
[inputs]: Add python-magic.
| Ricardo Wurmus | 2018-06-13 | 1 | -2/+3 |
| * | gnu: r-seurat: Update to 2.3.2.•••* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.2.
[propagated-inputs]: Add r-hdf5r.
| Ricardo Wurmus | 2018-06-13 | 1 | -2/+3 |
| * | gnu: r-s4vectors: Update to 0.18.3.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.3.
| Ricardo Wurmus | 2018-06-13 | 1 | -2/+2 |
| * | gnu: r-biocviews: Update to 1.48.1.•••* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.1.
| Ricardo Wurmus | 2018-06-13 | 1 | -2/+2 |
| * | gnu: rcas-web: Update to 0.0.5.•••* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.5.
| Ricardo Wurmus | 2018-06-08 | 1 | -2/+2 |
| * | gnu: r-rcas: Update to 1.6.0.•••* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.6.0.
[source]: Fetch from bioconductor.
[native-inputs]: Remove r-knitr.
[propagated-inputs]: Add r-biocgenerics, r-biostrings, r-cowplot, r-dbi,
r-ggseqlogo, r-knitr, r-pheatmap, r-proxy, r-rsqlite, and r-s4vectors.
| Ricardo Wurmus | 2018-06-07 | 1 | -17/+25 |
| * | gnu: star: Update to 2.6.0c.•••* gnu/packages/bioinformatics.scm (star): Update to 2.6.0c.
[source]: Fetch from git.
| Ricardo Wurmus | 2018-06-07 | 1 | -6/+7 |
| * | Merge branch 'master' into core-updates | Ricardo Wurmus | 2018-06-05 | 1 | -0/+51 |
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| | * | gnu: Add sjcount.•••* gnu/packages/bioinformatics.scm (sjcount): New variable.
| Ricardo Wurmus | 2018-06-05 | 1 | -0/+51 |
| * | | gnu: dropseq-tools: Remove failing phase.•••* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Delete
"generate-jar-indices" phase.
| Ricardo Wurmus | 2018-06-05 | 1 | -0/+3 |
| * | | gnu: pigx-scrnaseq: Use only one variant of Picard.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"java-picard" with "java-picard-2.10.3".
| Ricardo Wurmus | 2018-06-05 | 1 | -1/+1 |
| * | | gnu: java-picard: Delete failing build phase.•••* gnu/packages/bioinformatics.scm (java-picard)[arguments]: Delete
"generate-jar-indices" phase.
| Ricardo Wurmus | 2018-06-05 | 1 | -0/+2 |
| * | | gnu: java-picard-1.113: Delete failing build phase.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Delete
"generate-jar-indices" build phase.
| Ricardo Wurmus | 2018-06-05 | 1 | -0/+2 |
| * | | gnu: java-picard-2.10.3: Delete failing build phase.•••* gnu/packages/bioinformatics.scm (java-picard-2.10.3)[arguments]: Delete
generate-jar-indices phase.
| Ricardo Wurmus | 2018-06-05 | 1 | -0/+2 |
| * | | Merge branch 'master' into core-updates | Ricardo Wurmus | 2018-06-05 | 1 | -6/+6 |
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| | * | gnu: r-rtracklayer: Update to 1.40.3.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.3.
| Ricardo Wurmus | 2018-06-05 | 1 | -2/+2 |
| | * | gnu: r-methylkit: Update to 1.6.1.•••* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.1.
| Ricardo Wurmus | 2018-06-05 | 1 | -2/+2 |
| | * | gnu: r-bamsignals: Update to 1.12.1.•••* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.1.
| Ricardo Wurmus | 2018-06-05 | 1 | -2/+2 |
| * | | Merge branch 'master' into core-updates | Ricardo Wurmus | 2018-06-02 | 1 | -241/+232 |
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| | * | gnu: r-scater: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0.
[propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove
r-matrixstats and r-biomart.
| Ricardo Wurmus | 2018-06-02 | 1 | -4/+4 |
| | * | gnu: r-scran: Update to 1.8.2.•••* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2.
[propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray.
| Ricardo Wurmus | 2018-06-02 | 1 | -4/+5 |
| | * | gnu: r-delayedmatrixstats: Update to 1.2.0.•••* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0.
| Ricardo Wurmus | 2018-06-02 | 1 | -2/+2 |
| | * | gnu: r-singlecellexperiment: Update to 1.2.0.•••* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0.
| Ricardo Wurmus | 2018-06-02 | 1 | -2/+2 |
| | * | gnu: r-beachmat: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1.
[inputs]: Add zlib.
| Ricardo Wurmus | 2018-06-02 | 1 | -3/+4 |
| | * | gnu: r-rhdf5lib: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1.
[arguments]: Adjust substitutions.
| Ricardo Wurmus | 2018-06-02 | 1 | -8/+7 |
| | * | gnu: r-hdf5array: Update to 1.8.0.•••* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0.
| Ricardo Wurmus | 2018-06-02 | 1 | -2/+2 |
| | * | gnu: r-qvalue: Update to 2.12.0.•••* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0.
| Ricardo Wurmus | 2018-06-02 | 1 | -2/+2 |
