| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
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* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
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* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
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* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
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This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.
* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
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* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm,
gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm,
gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm,
gnu/packages/commencement.scm, gnu/packages/dictionaries.scm,
gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm,
gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm,
gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm,
gnu/packages/javascript.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm,
gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm,
gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm,
gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages
using 'trivial-build-system', use invoke where appropriate, raise exceptions
on errors, and otherwise return #t.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
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* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
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* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
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* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx): New variable.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
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* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
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* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
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* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
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* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
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* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
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* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
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* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
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* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
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* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
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