Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to
x86_64-linux.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
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* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
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* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
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* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
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* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
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* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
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* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
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* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
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* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9.
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* gnu/packages/admin.scm: Update URLs pointing to sourceforge.net.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/boost.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/compression.scm: Likewise.
* gnu/packages/cups.scm: Likewise.
* gnu/packages/djvu.scm: Likewise.
* gnu/packages/docbook.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fonts.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/graphviz.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/onc-rpc.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/popt.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/swig.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15.
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* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference
to non-existing "lapacke" output.
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* gnu/packages/bioinformatics.scm (eigensoft): New variable.
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* gnu/packages/bioinformatics.scm (ribotaper): New variable.
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* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12.
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* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New
variables.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
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* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to
x86_64-linux and mips64el-linux.
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* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11.
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* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
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* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field.
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* gnu/packages/bioinformatics.scm (multiqc): New variable.
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* gnu/packages/bioinformatics.scm (bits): New variable.
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* gnu/packages/bioinformatics.scm (emboss): New variable.
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* gnu/packages/bioinformatics.scm (r-edger): New variable.
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* gnu/packages/bioinformatics.scm (r-limma): New variable.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1.
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* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
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* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
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* gnu/packages/bioinformatics.scm (seek): New variable.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
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* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
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* gnu/packages/bioinformatics.scm (khmer): New variable.
* gnu/packages/patches/khmer-use-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
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* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
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