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1328 Commits

Author SHA1 Message Date
Ricardo Wurmus 02be818044
gnu: r-annotate: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0.
 2018-06-02 13:39:06 +02:00
Ricardo Wurmus 59f87b44da
Merge branch 'master' into core-updates 2018-05-31 13:23:49 +02:00
Ricardo Wurmus ce8b9e3b1c
gnu: r-seurat: Update to 2.3.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.1.
[propagated-inputs]: Remove r-gridextra; add r-reticulate.
 2018-05-31 13:21:31 +02:00
Ricardo Wurmus 3ca317359c
gnu: r-vegan: Update to 2.5-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-2.
 2018-05-31 13:21:31 +02:00
Mark H Weaver 1640f16e78
Merge branch 'master' into core-updates 2018-05-27 01:26:09 -04:00
Ricardo Wurmus a1b802454a
gnu: Add fastp. 
* gnu/packages/bioinformatics.scm (fastp): New variable.
 2018-05-24 17:49:32 +02:00
Mark H Weaver 9d10a63402
Merge branch 'master' into core-updates 2018-05-24 02:34:08 -04:00
Ricardo Wurmus a4ab65ee79
gnu: pigx-scrnaseq: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.4.
 2018-05-23 15:27:32 +02:00
Ricardo Wurmus 0f5ad3a1bc
gnu: bismark: Patch bismark2report before installing. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Patch file before
installing it.
 2018-05-22 16:05:41 +02:00
Mark H Weaver 0661758e13
Merge branch 'master' into core-updates 2018-05-21 13:22:32 -04:00
Tobias Geerinckx-Rice c61d822621
gnu: f-seq: Factorise ‘install’ phase. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Let-bind more.
 2018-05-19 05:30:11 +02:00
Tobias Geerinckx-Rice 4ca9581119
gnu: multiqc: Fix build. 
* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Add a
‘relax-requirements’ phase to fix building with python-matplotlib@2.2.
 2018-05-17 23:08:30 +02:00
Mark H Weaver 539bf8f2c0
Merge branch 'master' into core-updates 2018-05-17 01:00:50 -04:00
Ben Woodcroft 2c5289b263
gnu: diamond: Update to 0.9.22. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22.
 2018-05-12 11:01:21 +10:00
Ricardo Wurmus 126c9e3ff7
gnu: bismark: Update to 0.19.1. 
* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1.
[source]: Fetch from git; remove non-free software in snippet.
[arguments]: Update install phase.
 2018-05-09 18:37:33 +02:00
Ricardo Wurmus f895a7a4d4
gnu: trim-galore: Update to 0.4.5. 
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5.
[source]: Fetch from git.
[arguments]: Remove custom unpack phase.
 2018-05-09 18:37:33 +02:00
Marius Bakke 12bd588346
Merge branch 'master' into core-updates 2018-05-06 15:56:24 +02:00
Tobias Geerinckx-Rice a2cfe19041
gnu: Use HTTPS for www.boost.org. 
* gnu/packages/bioinformatics.scm (libgff)[license]: Use HTTPS.
* gnu/packages/boost.scm (boost-sync)[license]: Likewise.
(boost)[license]: Likewise.
[home-page]: Likewise, and use canonical ‘www’ subdomain.
 2018-05-01 06:51:15 +02:00
Mark H Weaver 3d5ad159b3
Merge branch 'master' into core-updates 2018-04-30 04:03:54 -04:00
Roel Janssen dad9556c5d
gnu: roary: Update to 3.12.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
 2018-04-28 01:52:52 +02:00
Roel Janssen d36d5229ed
gnu: star: Update to 2.6.0a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
 2018-04-28 01:24:10 +02:00
Roel Janssen 457fd268ff
gnu: multiqc: Update to 1.5. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
 2018-04-28 01:10:24 +02:00
Roel Janssen 4b93efec28
gnu: express: Link with shared protobuf library. 
* gnu/packages/bioinformatics.scm (express): Link with shared protobuf
  library.
 2018-04-28 01:07:15 +02:00
Roel Janssen 4ffa085875
gnu: bamtools: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
 2018-04-28 00:56:59 +02:00
Roel Janssen d0c75e73d4
gnu: taxtastic: Update to 0.8.5. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
 2018-04-28 00:43:16 +02:00
Ben Woodcroft 53ec1b7e8b
gnu: vsearch: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
 2018-04-27 23:20:00 +10:00
Ben Woodcroft 171cf56c2f
gnu: diamond: Update to 0.9.21. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
 2018-04-27 23:20:00 +10:00
Roel Janssen b43a9eb361
gnu: bedops: Update to 2.4.33. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
 2018-04-27 01:11:57 +02:00
Roel Janssen c829c5ea85
gnu: samtools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
 2018-04-27 01:11:47 +02:00
Roel Janssen cbd9f91c32
gnu: bcftools: Update to 1.8. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
 2018-04-27 01:11:42 +02:00
Roel Janssen 8df0267ad4
gnu: htslib: Update to 1.8. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
 2018-04-27 01:11:24 +02:00
Ricardo Wurmus 3d7f9cbe75
gnu: pigx-chipseq: Update to 0.0.15. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
 2018-04-22 23:00:51 +02:00
Ricardo Wurmus c36ce47635
gnu: r-seurat: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.0.
[propagated-inputs]: Add r-cluster, r-dosnow, r-fitdistrplus, r-foreach,
r-lmtest, r-png, and r-rann.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus aeca5f0c5b
gnu: r-scran: Update to 1.6.9. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 80323c3c13
gnu: r-hitc: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus b6d7deca55
gnu: r-ldblock: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fb1dcfac46
gnu: r-erma: Update to 0.10.1. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 8defca1d94
gnu: r-gprofiler: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus fc6d3e2606
gnu: r-ggbio: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 4207770218
gnu: r-dexseq: Update to 1.24.4. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
 2018-04-21 23:07:52 +02:00
Ricardo Wurmus 3db5d04ccc
gnu: r-vegan: Update to 2.5-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
 2018-04-21 23:07:52 +02:00
Mark H Weaver f89aa1521a
Merge branch 'master' into core-updates 2018-04-10 00:42:22 -04:00
Ricardo Wurmus 482959ffa4
gnu: sambamba: Update to 0.6.7-10-g223fa20. 
* 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.
 2018-04-06 17:12:15 +02:00
Ricardo Wurmus 262ee8eae2
gnu: htslib-for-sambamba: Fix build. 
* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
 2018-04-06 17:12:07 +02:00
Roel Janssen fdc306879b
gnu: Add delly. 
* 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>
 2018-03-30 10:48:01 -04:00
Ben Woodcroft f38ac742e6
gnu: mash: Update to 2.0. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft c7a8aa131d
gnu: mafft: Update to 7.394. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
 2018-03-30 12:18:35 +10:00
Ben Woodcroft 9a40b8d9b2
gnu: diamond: Update to 0.9.19. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
 2018-03-30 12:18:35 +10:00
Marius Bakke 5576cfabf3
Merge branch 'master' into core-updates 2018-03-29 17:34:41 +02:00
Roel Janssen e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
  [propagated-inputs]: Remove r-gridextra.
 2018-03-29 15:50:44 +02:00
Roel Janssen 53e42694e5
gnu: kaiju: Update to 1.6.2. 
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
  [inputs]: Add zlib.
 2018-03-29 15:40:52 +02:00
Mark H Weaver e3cfef22c4
gnu: Use invoke and return #t from all builders. 
* 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.
 2018-03-27 21:35:41 -04:00
Tobias Geerinckx-Rice 904c3a4e99
gnu: r-annotate: Update to 1.56.2. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
 2018-03-25 00:36:31 +01:00
Ricardo Wurmus 618050a126
gnu: r-bookdown: Do not propagate ghc-pandoc. 
This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.

* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
 2018-03-22 17:07:15 +01:00
Ricardo Wurmus 363ee7a3f4
gnu: pigx-chipseq: Update to 0.0.10. 
* 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.
 2018-03-21 11:52:56 +01:00
Ricardo Wurmus d7a11f1a8d
gnu: pigx-chipseq: Update to 0.0.9. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
 2018-03-20 19:47:37 +01:00
Mark H Weaver ac21be848a
Merge branch 'master' into core-updates 2018-03-20 14:22:06 -04:00
Ricardo Wurmus 4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
 2018-03-20 14:56:44 +01:00
Ricardo Wurmus 616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
 2018-03-20 12:20:51 +01:00
Mark H Weaver 647888845c
Merge branch 'master' into core-updates 2018-03-20 00:49:05 -04:00
Ricardo Wurmus 9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 096589035e
gnu: bismark: Fix references to gunzip. 
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
 2018-03-19 21:06:51 +01:00
Ricardo Wurmus 51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
 2018-03-19 21:06:50 +01:00
Ricardo Wurmus d8f08c85ad
gnu: pigx: Update to 0.0.2. 
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
 2018-03-19 16:55:43 +01:00
Ricardo Wurmus d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1. 
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
 2018-03-19 16:55:43 +01:00
Ricardo Wurmus 32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1. 
* 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.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1. 
* 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.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus fd757a8f21
gnu: pigx-chipseq: Use pandoc-1. 
* 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.
 2018-03-19 11:07:55 +01:00
Ricardo Wurmus 1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1. 
* 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.
 2018-03-19 11:07:54 +01:00
Mark H Weaver 9f388b1ee1
Merge branch 'master' into core-updates 2018-03-17 01:18:37 -04:00
Ricardo Wurmus c1c9cc664b
gnu: Add pigx. 
* gnu/packages/bioinformatics.scm (pigx): New variable.
 2018-03-16 15:40:31 +01:00
Ricardo Wurmus fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
 2018-03-16 15:40:31 +01:00
Mark H Weaver 6cbee49d66
gnu: All snippets report errors using exceptions, else return #t. 
* 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.
 2018-03-16 09:08:31 -04:00
Ricardo Wurmus 46264c73a6
gnu: Add pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
 2018-03-16 11:15:04 +01:00
Ricardo Wurmus b44437c549
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:01:07 +01:00
Ricardo Wurmus 80420f114c
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:00:31 +01:00
Leo Famulari 32cbbac11a
gnu: Add Diversitree. 
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
 2018-03-15 10:57:51 -04:00
Ricardo Wurmus 8c72ed923d
Merge branch 'master' into core-updates 2018-03-14 17:37:20 +01:00
Ludovic Courtès 189be331ac
build-system/gnu: Add 'bootstrap' phase. 
This factorizes what has become a widespread idiom.

* guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable.
(bootstrap): New procedure.
(%standard-phases): Add it after 'unpack'.
* guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap.
* guix/build/asdf-build-system.scm (%standard-phases/source)
(%standard-phases): Likewise.
* guix/build/cargo-build-system.scm (%standard-phases): Likewise.
* guix/build/cmake-build-system.scm (%standard-phases): Likewise.
* guix/build/dub-build-system.scm (%standard-phases): Likewise.
* guix/build/emacs-build-system.scm (%standard-phases): Likewise.
* guix/build/font-build-system.scm (%standard-phases): Likewise.
* guix/build/go-build-system.scm (%standard-phases): Likewise.
* guix/build/haskell-build-system.scm (%standard-phases): Likewise.
* guix/build/minify-build-system.scm (%standard-phases): Likewise.
* guix/build/ocaml-build-system.scm (%standard-phases): Likewise.
* guix/build/perl-build-system.scm (%standard-phases): Likewise.
* guix/build/python-build-system.scm (%standard-phases): Likewise.
* guix/build/r-build-system.scm (%standard-phases): Likewise.
* guix/build/ruby-build-system.scm (%standard-phases): Likewise.
* guix/build/scons-build-system.scm (%standard-phases): Likewise.
* guix/build/texlive-build-system.scm (%standard-phases): Likewise.
* guix/build/waf-build-system.scm (%standard-phases): Likewise.
* gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap.
(soundtouch, cuetools, bluez-alsa): Remove 'arguments'.
(cava)[arguments]: Replace 'bootstrap.
* gnu/packages/backup.scm (rdup): Remove 'bootstrap.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Replace
'bootstrap.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove
'arguments'.
* gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'.
* gnu/packages/crypto.scm (libb2): Remove #:phases.
* gnu/packages/databases.scm (guile-wiredtiger): Likewise.
* gnu/packages/debug.scm (stress-make): Remove 'bootstrap'.
* gnu/packages/documentation.scm (asciidoc): Likewise.
* gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'.
* gnu/packages/ftp.scm (weex): Remove 'arguments'.
* gnu/packages/game-development.scm (ois): Remove 'arguments'.
* gnu/packages/games.scm (pioneer): Remove 'bootstrap.
* gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap.
(arc-theme): Remove 'arguments'.
(faba-icon-theme): Remove 'bootstrap.
(arc-icon-theme): Remove 'arguments'.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/gtk.scm (guile-rsvg): Likewise.
* gnu/packages/guile.scm (mcron2): Remove 'bootstrap.
(guile-bash): Remove #:phases.
(guile-git): Remove 'bootstrap.
(guile-syntax-highlight): Remove 'arguments'.
(guile-sjson): Likewise.
* gnu/packages/java.scm (classpath-devel): Remove 'bootstrap.
* gnu/packages/kodi.scm (libdvdnav/kodi)
(libdvdread/kodi, libdvdcss/kodi): Likewise.
* gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'.
* gnu/packages/libusb.scm (hidapi): Likewise.
* gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to
'patch-stuff'; move it before 'bootstrap', without autoreconf
invocation.
(eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh'
invocation; move it before 'bootstrap.
(gpm): Replace 'bootstrap'.
(f2fs-tools): Remove 'arguments'.
(rng-tools): Remove #:phases.
* gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to
'copy-intltool-makefile'; remove "autoreconf" invocation and move before
'bootstrap'.
(libmesode): Remove 'arguments'.
(libstrophe): Likewise.
* gnu/packages/microcom.scm (microcom): Likewise.
* gnu/packages/networking.scm (libnet): Remove 'bootstrap.
* gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'.
* gnu/packages/package-management.scm (guix): Replace 'bootstrap.
* gnu/packages/sawfish.scm (librep): Remove 'arguments'.
* gnu/packages/version-control.scm (findnewest): Likewise.
* gnu/packages/video.scm (liba52, handbrake, motion): Replace
'bootstrap.
* gnu/packages/web.scm (fcgiwrap): Remove #:phases.
(tidy): Replace 'bootstrap.
(gumbo-parser): Remove #:phases.
* gnu/packages/wget.scm (wget2): Replace 'bootstrap.
* gnu/packages/wm.scm (i3lock-color): Remove #:phases.
* gnu/packages/xdisorg.scm (xclip): Likewise.
* gnu/packages/xml.scm (libxls): Replace 'bootstrap'.
* gnu/packages/xorg.scm (xf86-video-freedreno)
(xf86-video-intel): Remove #:phases.
* gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
 2018-03-11 22:04:40 +01:00
Ricardo Wurmus fb94174fc3
gnu: Add pigx-bsseq. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus 531afc8a89
gnu: Add pigx-chipseq. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus a539ad867d
gnu: r-rhdf5lib: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
 2018-03-09 11:40:59 +01:00
Ricardo Wurmus 22a0c65969
gnu: Add r-phangorn. 
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
 2018-03-08 23:31:56 +01:00
Ricardo Wurmus 53cc59a1d8
gnu: r-ape: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
 2018-03-08 23:31:55 +01:00
Ricardo Wurmus 84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f. 
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
 2018-03-08 18:53:49 +01:00
Ricardo Wurmus 0bdd5b8ab7
gnu: Add pigx-rnaseq. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
 2018-03-07 23:25:36 +01:00
Ricardo Wurmus c072cf57b9
gnu: samtools: Update to 1.7. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus 727d847980
gnu: htslib: Update to 1.7. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus e325c89076
gnu: r-rhdf5: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
 2018-03-06 16:03:04 +01:00
Efraim Flashner da49d13710
gnu: piranha: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner d9a069c2d9
gnu: libdivsufsort: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner 5110672474
gnu: seek: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner b1d4026dfb
gnu: r-dropbead: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
 2018-03-04 12:05:10 +02:00
Ricardo Wurmus 1adeef3194
gnu: Add dropseq-tools. 
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
 2018-03-03 21:28:05 +01:00
Ricardo Wurmus 72299db9fe
gnu: Add java-picard-2.10.3. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
 2018-03-03 21:28:02 +01:00
Ricardo Wurmus 719fa958f3
gnu: Add java-htsjdk-2.10.1. 
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
 2018-03-03 21:27:59 +01:00
Ricardo Wurmus 9a599c17b7
gnu: Add java-htsjdk-latest. 
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
 2018-03-03 21:27:57 +01:00
Ricardo Wurmus 9ac7db1830
gnu: Add java-biojava-alignment-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
 2018-03-03 21:27:56 +01:00
Ricardo Wurmus 5528f9e8f0
gnu: Add java-biojava-phylo-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
 2018-03-03 21:27:53 +01:00
Ricardo Wurmus e44da58c16
gnu: Add java-biojava-core-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
 2018-03-03 21:27:51 +01:00
Ricardo Wurmus 22c09c335b
gnu: Add java-biojava-alignment. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
 2018-03-03 21:27:48 +01:00
Ricardo Wurmus b28c803708
gnu: Add java-biojava-phylo. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
 2018-03-03 21:27:46 +01:00
Ricardo Wurmus 10645b9212
gnu: Add java-forester-1.005. 
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
 2018-03-03 21:27:44 +01:00
Ricardo Wurmus f09d16e594
gnu: Add java-forester. 
* gnu/packages/bioinformatics.scm (java-forester): New variable.
 2018-03-03 21:27:41 +01:00
Ricardo Wurmus 5fef15e506
gnu: Add java-biojava-core. 
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
 2018-03-03 21:27:36 +01:00
Ricardo Wurmus bd975831c6
gnu: Add fastqc. 
* gnu/packages/bioinformatics.scm (fastqc): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus 3ede1550e8
gnu: cutadapt: Update to 1.16. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus 9aaf2813e2
gnu: r-scran: Update to 1.6.8. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 6a0e13906b
gnu: r-wgcna: Update to 1.63. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 61cbd49b30
gnu: r-topgo: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 535014ce60
gnu: r-genomicranges: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus eb8971b742
gnu: r-limma: Update to 3.34.9. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 22d96920d3
gnu: r-edger: Update to 3.20.9. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 99e4b11d81
gnu: r-shortread: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus b180893289
gnu: r-dexseq: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
 2018-03-01 21:28:52 +01:00
Ricardo Wurmus 65c9d25739
gnu: r-qtl: Update to 1.42-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
 2018-02-22 11:18:03 +01:00
Ricardo Wurmus 79c6af13d0
gnu: r-delayedmatrixstats: Update to 1.0.3. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus 59b2864d6c
gnu: r-scater: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus d578278e35
gnu: r-gviz: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus ca7855fcd2
gnu: r-gprofiler: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 8877ab432e
gnu: r-ensembldb: Update to 2.2.2. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ebec98ae1d
gnu: r-seurat: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 3118b28644
gnu: r-qtl: Update to 1.42-7. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 824c200475
gnu: r-genomicranges: Update to 1.30.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus e8484711c6
gnu: r-getopt: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 9800f7d9e8
gnu: r-bookdown: Update to 0.7. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ff9d1a2f0c
Merge branch 'master' into core-updates 2018-02-18 00:39:25 +01:00
Ben Woodcroft 369eee8763
gnu: vsearch: Update to 2.7.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1.
 2018-02-17 12:44:29 +10:00
Mark H Weaver 150062f190
Merge branch 'master' into core-updates 2018-02-16 13:14:26 -05:00
Ben Woodcroft 5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Ricardo Wurmus 152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus 3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus 05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Mark H Weaver 932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Ben Woodcroft 119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Mark H Weaver 288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Ricardo Wurmus 97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 26e3e28cc9
gnu: r-seurat: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0.
[propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 53f0dea9d7
gnu: r-msnbase: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus b1f2753627
gnu: r-methylkit: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00