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* Merge branch 'master' into core-updatesLeo Famulari2018-01-11
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| * gnu: seqmagick: Use 'pypi-uri'.Ben Woodcroft2018-01-10
| | | | | | | | * gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
| * gnu: mafft: Update to 7.313.Ben Woodcroft2018-01-10
| | | | | | | | | | * gnu/packages/bioinformatics.scm (mafft): Update to 7.313. [source]: Use HTTPS URI.
| * gnu: seqmagick: Update to 0.7.0.Ben Woodcroft2018-01-09
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0. Use python-3. [arguments]: Remove replacement phase for check. [inputs]: Add biopython. Remove python2-biopython-1.66. (python2-biopython-1.66): Remove variable.
* | Merge branch 'master' into core-updatesLeo Famulari2018-01-03
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| * gnu: htslib: Mark up description.Tobias Geerinckx-Rice2018-01-02
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
| * gnu: ribotaper: Wrap executables.Ricardo Wurmus2018-01-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase "wrap-executables".
| * gnu: python-pysam: Update to 0.13.0.Tobias Geerinckx-Rice2018-01-02
| | | | | | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.13.0.
| * gnu: htslib: Update to 1.6.Tobias Geerinckx-Rice2018-01-02
| | | | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
* | Merge remote-tracking branch 'origin/master' into core-updatesEfraim Flashner2017-12-31
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| * gnu: vsearch: Update to 2.6.2.Ben Woodcroft2017-12-27
| | | | | | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.2.
| * gnu, doc: Use HTTPS for cran.r-project.org home pages.Tobias Geerinckx-Rice2017-12-24
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm) (r-maldiquant, r-gprofiler)[home-page]: Use HTTPS. * gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape) (r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle) (r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim) (r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken) (r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise. * gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab) [home-page]: Likewise. * gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise. * gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign) (r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability) (r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr) (r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports) (r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops) (r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options) (r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel) (r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3) (r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots) (r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools) (r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp) (r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn) (r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]: Likewise. * gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]: Likewise. * doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
| * gnu: Update r-mutationalpatterns to 1.4.2.Roel Janssen2017-12-22
| | | | | | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
* | Merge branch 'master' into core-updatesLeo Famulari2017-12-21
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| * gnu: r-biomart: Update to 2.34.1.Ricardo Wurmus2017-12-19
| | | | | | | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1. [propagated-inputs]: Add r-httr.
| * gnu: r-gviz: Update to 1.22.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
| * gnu: r-gqtlstats: Update to 1.10.1.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
| * gnu: r-rtracklayer: Update to 1.38.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
| * gnu: r-limma: Update to 3.34.4.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
| * gnu: r-edger: Update to 3.20.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
| * gnu: r-biocstyle: Update to 2.6.1.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
| * gnu: r-dexseq: Update to 1.24.2.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
| * gnu: r-vegan: Update to 2.4-5.Ricardo Wurmus2017-12-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
* | gnu: Remove redundant cmake libdir configure flags.Efraim Flashner2017-12-19
|/ | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Remove CMAKE_INSTALL_LIBDIR flag. * gnu/packages/calendar.scm (libical): Same. * gnu/packages/engineering.scm (kicad): Same. * gnu/packages/games.scm (openrct2, mgba): Same. * gnu/packages/gl.scm (virtualgl): Same. * gnu/packages/image-processing.scm (mia): Same. * gnu/packages/linux.scm (rdma-core): Same. * gnu/packages/machine-learning.scm (dlib): Same. * gnu/packages/maths.scm (lapack, superlu, z3): Same. * gnu/packages/password-utils.scm (keepassxc): Same. * gnu/packages/photo.scm (darktable): Same. * gnu/packages/rdesktop.scm (freerdp): Same.
* gnu: r-seurat: Update to 2.1.0.Ricardo Wurmus2017-12-18
| | | | | | | * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0. [propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica, r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr, r-rcppeigen, r-fastica.
* gnu: r-seurat: Fix ModularityOptimizer.jar.Ricardo Wurmus2017-12-18
| | | | | * gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class attribute in manifest.
* gnu: bedtools: Update to 2.27.1.Ben Woodcroft2017-12-15
| | | | * gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
* gnu: diamond: Update to 0.9.14.Ben Woodcroft2017-12-14
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
* gnu: Switch to using the version-major procedure.Christopher Baines2017-12-11
| | | | | | | * gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major. (hmmer)[source]: Switch to using version-major. (pidgin)[native-search-paths]: Switch to using version-major. (r-minimal)[source]: Switch to using version-major.
* gnu: bedtools-2.18: Fix build.Ricardo Wurmus2017-12-09
| | | | | | | * gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom install phase. Reported by Mark H Weaver <mhw@netris.org>.
* gnu: bedtools: Update to 2.27.0.Ricardo Wurmus2017-12-06
| | | | | * gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0. [arguments]: Remove custom "install" phase; specify prefix.
* gnu: Add kallisto.Ricardo Wurmus2017-12-03
| | | | * gnu/packages/bioinformatics.scm (kallisto): New variable.
* gnu: jellyfish: Update to 2.2.7.Ricardo Wurmus2017-11-30
| | | | | | * gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7. [native-inputs]: Add pkg-config. [inputs]: Add htslib.
* gnu: r-annotationhub: Update to 2.10.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
* gnu: r-msnid: Update to 1.12.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
* gnu: r-maldiquant: Update to 1.17.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
* gnu: r-genomicalignments: Update to 1.14.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
* gnu: r-limma: Update to 3.34.2.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
* gnu: r-variantannotation: Update to 1.24.2.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
* gnu: r-getopt: Update to 1.20.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
* gnu: r-gseabase: Update to 1.40.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
* gnu: r-dexseq: Update to 1.24.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
* gnu: r-deseq2: Update to 1.18.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
* gnu: r-annotate: Update to 1.56.1.Ricardo Wurmus2017-11-30
| | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
* gnu: metabat: Use scons-build-system.Arun Isaac2017-11-30
| | | | * gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
* gnu: Update r-mutationalpatterns to 1.4.1.Roel Janssen2017-11-29
| | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
* gnu: Add r-copynumber.Roel Janssen2017-11-29
| | | | * gnu/packages/bioinformatics.scm (r-copynumber): New variable.
* gnu: Add java-picard-1.113.Ricardo Wurmus2017-11-27
| | | | * gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
* gnu: Add java-picard.Ricardo Wurmus2017-11-27
| | | | * gnu/packages/bioinformatics.scm (java-picard): New variable.
* gnu: java-htsjdk: Update to 2.3.0.Ricardo Wurmus2017-11-27
| | | | | | | | * gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0. [arguments]: Build with JDK 8. [inputs]: Add java-ngs, java-snappy, java-commons-compress, java-commons-logging-minimal, java-commons-jexl-2, and java-xz. [native-inputs]: Add java-testng.
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