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2022-10-31gnu: Fix various lint issues in synopsis and descriptions....* gnu/packages/android.scm (etc1tool)[synopsis]: Drop trailing period. * gnu/packages/bioinformatics.scm (mudskipper)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-async-log-attributes-1)[synopsis]: Likewise. (rust-atomic-polyfill-1)[synopsis]: Likewise. (rust-modifier-0.1)[synopsis]: Likewise. (rust-openssl-macros-0.1)[synopsis]: Likewise. (rust-syn-mid-0.5)[synopsis]: Likewise. (rust-toml-edit-0.14)[synopsis]: Likewise. (rust-valuable-derive-0.1)[synopsis]: Likewise. (rust-inflections-1)[synopsis]: Likewise. * gnu/packages/databases.scm (python-databases)[synopsis]: Likewise. * gnu/packages/games.scm (liquidwar6)[synopsis]: Likewise. * gnu/packages/golang.scm (go-golang.org-x-sync-errgroup)[synopsis]: Likewise. * gnu/packages/guile-xyz.scm (guile-config)[synopsis]: Likewise. * gnu/packages/haskell-web.scm (ghc-hxt-xpath)[synopsis]: Likewise. * gnu/packages/haskell-xyz.scm (ghc-string-qq)[synopsis]: Likewise. * gnu/packages/machine-learning.scm (python-lap)[synopsis]: Likewise. (python-pyro-api)[synopsis]: Likewise. * gnu/packages/messaging.scm (python-librecaptcha)[synopsis]: Likewise. * gnu/packages/python-check.scm (python-pytest-cram)[synopsis]: Likewise. * gnu/packages/python-web.scm (python-jschema-to-python)[synopsis]: Likewise. (python-sarif-om)[synopsis]: Likewise. (python-socksio)[synopsis]: Likewise. (python-msrest)[synopsis]: Likewise. * gnu/packages/tor.scm (torsocks)[synopsis]: Likewise. * gnu/packages/cran.scm (r-rlist)[synopsis]: Remove leading article. * gnu/packages/crates-io.scm (rust-clippy-lints-0.0.153)[synopsis]: Likewise. (rust-simplelog-0.11)[synopsis]: Likewise. * gnu/packages/samba.scm (wsdd)[synopsis]: Likewise. * gnu/packages/crates-io.scm (rust-spki-0.4)[synopsis]: Remove trailing whitespace. * gnu/packages/golang.scm (go-github-com-mattn-go-zglob)[description]: Remove leading whitespace. * gnu/packages/haskell-check.scm (ghc-crypto-cipher-tests)[description]: Likewise. * gnu/packages/lisp-xyz.scm (sbcl-ctype)[synopsis]: Remove trailing whitespace. * gnu/packages/mpi.scm (openmpi-thread-multiple)[description]: Remove leading whitespace. * gnu/packages/node-xyz.scm (node-string-decoder)[synopsis]: Remove trailing whitespace. Vagrant Cascadian
2022-10-28gnu: flair: Update to 1.6.4....* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4. [propagated-inputs]: Add python-numpy and python-scipy. Ricardo Wurmus
2022-10-28gnu: flair: Set R_HOME....* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME. Ricardo Wurmus
2022-10-28gnu: flair: Add missing R package....* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm. Ricardo Wurmus
2022-10-27gnu: flair: Add missing R packages....* gnu/packages/bioinformatics.scm (flair)[propagated-inputs]: Add python-rpy2. [inputs]: Add r-minimal, r-deseq2, r-drimseq, r-ggplot2, r-lazyeval, r-qqman, and r-rlang. [arguments]: Add phase "wrap-executable". Ricardo Wurmus
2022-10-27gnu: Add python-multivelo....* gnu/packages/bioinformatics.scm (python-multivelo): New variable. Mădălin Ionel Patrașcu
2022-10-27gnu: Add r-seuratwrappers....* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable. Hong.Li@mdc-berlin.de
2022-10-24gnu: Various typo fixes....* gnu/packages/emacs-xyz.scm (emacs-popup-kill-ring)[description]: Fix very sneaky "This packages" variant. Thanks to nckhexen! * gnu/packages/bioinformatics.scm (r-icellnet)[description]: Fix use of "allows to". * gnu/packages/check.scm (python-pytest-freezegun)[description]: Ditto. * gnu/packages/linux.scm (tp-smapi-module)[description]: Ditto. * gnu/packages/mail.scm (procmail): Ditto. * gnu/packages/maths.scm (maxima): Ditto. * gnu/packages/samba.scm (wsdd)[description]: Ditto. * gnu/packages/ssh.scm (openssh): Ditto. Vagrant Cascadian
2022-10-23gnu: Fix typos....* gnu/packages/emacs-xyz.scm (emacs-piem)[description]: Fix use of "This packages". * gnu/packages/tex.scm (texlive-hardwrap)[description]: Fix spelling of "arbitrary". * gnu/packages/cran.scm (r-shinymanager)[description]: Fix spelling of "authentication". * gnu/packages/lisp-xyz.scm (sbcl-utils-kt)[description]: Fix spelling of "developed". * gnu/packages/crates-io.scm (rust-fs-utils-1)[description]: Fix spelling of "filesystem". [synopsis]: Likewise. * gnu/packages/haxe.scm (neko)[description]: Fix spelling of "functions". * gnu/packages/animation.scm (swftools)[description]: Fix needless pluralization of "information". * gnu/packages/lisp-xyz.scm (sbcl-slot-extra-options)[description]: Fix spelling of "inheritance". * gnu/packages/emacs-xyz.scm (emacs-js-comint)[description]: Fix spelling of "interpreter". * gnu/packages/coq.scm (coq-mathcomp-finmap)[description]: Fix spelling of "library". * gnu/services/lightdm.scm (lightdm-configuration): Fix spelling of "mechanism". * gnu/packages/emacs-xyz.scm (emacs-citar-org-roam)[synopsis]: Fix spelling of "package". * gnu/packages/games.scm (freerct)[description]: Fix spelling of "responsibilities". * gnu/packages/statistics.scm (r-mixedpower)[description]: Fix spelling of "separate". * gnu/packages/accessibility.scm (espeakup)[description]: Fix spelling of "speech". * gnu/packages/bioinformatics.scm (r-skitools)[synopsis]: Fix spelling of "utilities". * gnu/packages/golang.scm (go-github-com-savsgio-gotils)[synopsis]: Fix spelling of "utilities". [description]: Likewise. * gnu/system.scm (boot-file-system-service os): Fix spelling of "utilities". Vagrant Cascadian
2022-10-08gnu: pigx-sars-cov-2: Update to 0.0.8....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.8. [arguments]: Add build phase 'unpack-databases; enable tests. [native-inputs]: Add origins for databases; remove automake and autoconf. [inputs]: Add r-data-table, r-deconvr, r-htmltools, r-jsonlite, r-knitr, and r-mass. Ricardo Wurmus
2022-10-06gnu: plink: Change origin URL....pngu.mgh.harvard.edu seems to time out. * gnu/packages/bioinformatics.scm (plink)[origin]. Change URL. Christopher Baines
2022-10-05gnu: Add megahit....* gnu/packages/bioinformatics.scm (megahit): New variable. Ricardo Wurmus
2022-10-05gnu: Add cd-hit-auxtools....* gnu/packages/bioinformatics.scm (cd-hit-auxtools): New variable. Ricardo Wurmus
2022-10-05gnu: cd-hit: Update to 4.8.1....* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.8.1. [arguments]: Do not use quasiquote; remove trailing #T from build phases. [inputs]: Add zlib. Ricardo Wurmus
2022-10-04gnu: kaiju: Update to 1.9.0....* gnu/packages/bioinformatics.scm (kaiju): Update to 1.9.0. [arguments]: Use gexps; wrap scripts in install phase. [inputs]: Add bzip2, coreutils, curl, gawk, guile-3.0, gzip, python-wrapper, tar, and wget. Ricardo Wurmus
2022-09-30gnu: salmon: Update to 1.9.0....* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0. [arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish itlib headers. [inputs]: Use new label-less list; move pufferfish origin from here... [native-inputs]: ...to here. Ricardo Wurmus
2022-09-30gnu: Add centrifuge....* gnu/packages/bioinformatics.scm (centrifuge): New variable. Ricardo Wurmus
2022-09-29gnu: blast+: Build reproducibly....Fixes <https://issues.guix.gnu.org/42141>. * gnu/packages/bioinformatics.scm (blast+)[source]: Do not record kernel version and use fix set of random numbers. Ricardo Wurmus
2022-09-26gnu: Add r-compgenomrdata....* gnu/packages/bioinformatics.scm (r-compgenomrdata): New variable. Ricardo Wurmus
2022-09-23gnu: Add mudskipper....* gnu/packages/bioinformatics.scm (mudskipper): New variable. Ricardo Wurmus
2022-09-21gnu: python-cooler: Skip broken test....* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add another patch for tests/test_util.py. Ricardo Wurmus
2022-09-21gnu: python-cooler: Do not use flake8....* gnu/packages/bioinformatics.scm (python-cooler)[arguments]: Add build phase 'do-not-use-flake8. Ricardo Wurmus
2022-09-21gnu: Add r-chromunity....* gnu/packages/bioinformatics.scm (r-chromunity): New variable. Ricardo Wurmus
2022-09-21gnu: Add r-skitools....* gnu/packages/bioinformatics.scm (r-skitools): New variable. Ricardo Wurmus
2022-09-21gnu: Add r-gchain....* gnu/packages/bioinformatics.scm (r-gchain): New variable. Ricardo Wurmus
2022-09-21gnu: Add r-gtrack....* gnu/packages/bioinformatics.scm (r-gtrack): New variable. Ricardo Wurmus
2022-09-21gnu: Add r-bamutils....* gnu/packages/bioinformatics.scm (r-bamutils): New variable. Ricardo Wurmus
2022-09-21gnu: Add r-gutils....* gnu/packages/bioinformatics.scm (r-gutils): New variable. Ricardo Wurmus
2022-09-20gnu: python-pyvcf: Update to 0.6.8-0.476169c....* gnu/packages/bioinformatics.scm (python-pyvcf): Update to 0.6.8-0.476169c. Ricardo Wurmus
2022-09-20gnu: python-pyvcf: Use older setuptools....* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Replace python-setuptools with python-setuptools-for-tensorflow. Ricardo Wurmus
2022-09-15gnu: catch-framework2: Rename variable to catch2....Automated with: git grep -l catch-framework2 | xargs sed 's/catch-framework2/catch2/g' -i Maxim Cournoyer
2022-09-13gnu: kraken2: Update to 2.1.2....* gnu/packages/bioinformatics.scm (kraken2): Update to 2.1.2. Ricardo Wurmus
2022-09-10gnu: Add comments to the bottom of a few package modules....This will hopefully discourage patches which add new packages to the bottom of files, as this increases the likelihood of conflicts when applying patches. If there are more specific ways that packages should be arranged in specific modules, this message can be updated accordingly. * gnu/packages/bioconductor.scm: Add comment discouraging adding packages to the bottom of the file. * gnu/packages/bioinformatics.scm: ditto. * gnu/packages/cran.scm: ditto. * gnu/packages/crates-io.scm: ditto. * gnu/packages/emacs-xyz.scm: ditto. * gnu/packages/golang.scm: ditto. * gnu/packages/guile-xyz.scm: ditto. * gnu/packages/haskell-xyz.scm: ditto. * gnu/packages/java.scm: ditto. * gnu/packages/julia-xyz.scm: ditto. * gnu/packages/lisp-xyz.scm: ditto. * gnu/packages/ocaml.scm: ditto. * gnu/packages/perl.scm: ditto. * gnu/packages/python-science.scm: ditto. * gnu/packages/python-xyz.scm: ditto. * gnu/packages/ruby.scm: ditto. * gnu/packages/tex.scm: ditto. Christopher Baines
2022-09-07gnu: tombo: Disable tests....* gnu/packages/bioinformatics.scm (tombo)[arguments]: New field. Marius Bakke
2022-08-31gnu: pigx-bsseq: Update to 0.1.8....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.8. Ricardo Wurmus
2022-08-30gnu: r-dyngen: Update to 1.0.4....* gnu/packages/bioinformatics.scm (r-dyngnen): Update to 1.0.4. [source]: Change to cran-uri source. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2022-08-23gnu: Add flair....* gnu/packages/bioinformatics.scm (flair): New variable. Ricardo Wurmus
2022-08-23gnu: python-mappy: Update to 2.24....* gnu/packages/bioinformatics.scm (python-mappy): Update to 2.24. Ricardo Wurmus
2022-08-18gnu: Add r-kbet....* gnu/packages/bioinformatics.scm (r-kbet): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-biogo....* gnu/packages/bioinformatics.scm (go-github-com-biogo-biogo): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-fai....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-fai): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-csi....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-csi): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-cram....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-bgzf....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bgzf): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-tabix....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-tabix): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-sam....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-sam): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-hts-bam....* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-store-step....* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-step): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-store-llrb....* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-llrb): New variable. Ricardo Wurmus
2022-08-16gnu: Add go-github-com-biogo-store-kdtree....* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree): New variable. Ricardo Wurmus