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2022-12-18gnu: python-scanpy: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases; move pytest arguments to #:test-flags; add 'pretend-version phase; replace custom 'check phase with 'delete-bad-tests phase.
2022-12-18gnu: python-multivelo: Simplify with pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases.
2022-12-14gnu: bedtools-2.18: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp. [native-inputs]: Drop package label.
2022-12-13gnu: bedops: Update to 2.4.41.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41. [arguments]: Remove trailing #T from build phases; do not set BINDIR in make-flags; set CC; replace 'install phase. [native-inputs]: Add diffutils, perl, and which.
2022-12-13gnu: tophat: Remove trailing #T from build phases and snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from build phases.
2022-12-13gnu: python-bx-python: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'build-extensions and 'disable-cython-doctests. [native-inputs]: Replace python-nose with python-pytest.
2022-12-13gnu: bioawk: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify 'install phase.
2022-12-13gnu: blasr-libcpp: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: pbbam: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13gnu: pbbam: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
2022-12-13gnu: pbcopper: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
2022-12-13gnu: bedtools: Remove unnecessary quasiquotation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote. [native-inputs]: Drop input label.
2022-12-13gnu: bamutils: Update to 1.0.15.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15. [arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags. [native-inputs]: Update libstatgen.
2022-12-13gnu: bamtools: Update to 2.5.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2. [arguments]: Enable tests; remove extra phases. [inputs]: Add jsoncpp. [native-inputs]: Add pkg-config.
2022-12-13gnu: aragorn: Update to 1.2.41.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.41. [source]: Fetch C source file from new location. [arguments]: Drop trailing #T in build phases; use gexp. [native-inputs]: Add origin for man page. [home-page]: Update to new home page. [license]: Update to GPLv3+.
2022-12-13gnu: cnvkit: Update to 0.9.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9. [build-system]: Use pyproject-build-system. [arguments]: Relax restriction on python-joblib. [propagated-inputs]: Add python-pomegranate and python-scikit-learn.
2022-12-13gnu: seqmagick: Update to 0.8.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.4. [build-system]: Use pyproject-build-system. [inputs]: Add python-pygtrie. [native-inputs]: Replace python-nose with python-pytest.
2022-12-13gnu: python-cgatcore: Update to 0.6.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.14. [build-system]: Use pyproject-build-system. [arguments]: Disable broken tests with #:test-flags; do not replace 'check phase; add phase 'sqlite-compatibility. [native-inputs]: Drop input labels.
2022-12-13gnu: python-dna-features-viewer: Update to 3.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dna-features-viewer): Update to 3.1.1. [build-system]: Use pyproject-build-system. [arguments]: Add build phase to fix a compatibility problem with biopython. [propagated-inputs]: Add python-packaging.
2022-12-13gnu: python-hicexplorer: Update to 3.7.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2. [build-system]: Use pyproject-build-system. [arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a dependency on an unlicensed package; add phase "fix-references"; add phase "run-only-low-mem-tests". [propagated-inputs]: Remove python-configparser and python-six; add python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz, python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn, python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks, python-scikit-learn, and python-tqdm. [native-inputs]: Add graphviz.
2022-12-13gnu: python-pygenometracks: Update to 3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.5. [build-system]: Use pyproject-build-system. [arguments]: Quote phases instead of full list of arguments; remove trailing #T from build phase.
2022-12-13gnu: python-hicmatrix: Update to 16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16. [build-system]: Use pyproject-build-system. [arguments]: Shuffle the quote.
2022-12-13gnu: python-biopython: Update to 1.80.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80. [build-system]: Use pyproject-build-system. [arguments]: Remove trailing #T from build phase.
2022-12-12gnu: bioperl-minimal: Remove trailing #T from build phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove trailing #T from build phase.
2022-12-02gnu: python-biom-format: Update to 2.1.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.12. [arguments]: Remove "relax" phase; update "disable-broken-tests" phase. [propagated-inputs]: Add python-scikit-bio.
2022-12-02gnu: Add python-scikit-bio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
2022-12-02gnu: python-pairtools: Update to 1.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2. [source]: Update Github URL. [arguments]: Update patch in "fix-references" phase. [native-inputs]: Remove python-nose. [inputs]: Remove. [propagated-inputs]: Add python-bioframe, python-pandas, python-pysam, python-pyyaml, and python-scipy. [home-page]: Update.
2022-12-02gnu: python-pairtools: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests conditionally.
2022-12-02gnu: python-pybedtools: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use pyproject-build-system. [arguments]: Import (guix build pyproject-build-system).
2022-12-02gnu: python-htsget: Update to 0.2.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6. [build-system]: Use pyproject-build-system.
2022-12-02gnu: python-cellbender: Update to 0.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2. [build-system]: Use pyproject-build-system.
2022-12-02gnu: Add python-fanc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fanc): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-12-02gnu: Add python-genomic-regions.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
2022-11-25gnu: Add r-btools.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-btools): New variable.
2022-11-17gnu: r-circus: Update to 0.1.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-circus): Update to 0.1.7. [properties]: Add upstream-name property. [propagated-inputs]: Add r-biocgenerics, r-genomeinfodb, and r-rtracklayer.
2022-11-15gnu: Add r-disgenet2r.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
2022-11-09gnu: Add r-pando.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-pando): New variable.
2022-11-04gnu: Add python-cooltools.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
2022-11-04gnu: Add python-bioframe.Mădălin Ionel Patrașcu
X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-bioframe): New variable.
2022-11-04gnu: r-dyngen: Update to 1.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dyngen): Update to 1.0.5.
2022-10-31gnu: Fix various lint issues in synopsis and descriptions.Vagrant Cascadian
* 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.
2022-10-28gnu: flair: Update to 1.6.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flair): Update to 1.6.4. [propagated-inputs]: Add python-numpy and python-scipy.
2022-10-28gnu: flair: Set R_HOME.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
2022-10-28gnu: flair: Add missing R package.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
2022-10-27gnu: flair: Add missing R packages.Ricardo Wurmus
* 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".
2022-10-27gnu: Add python-multivelo.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
2022-10-27gnu: Add r-seuratwrappers.Hong.Li@mdc-berlin.de
* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
2022-10-24gnu: Various typo fixes.Vagrant Cascadian
* 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.
2022-10-23gnu: Fix typos.Vagrant Cascadian
* 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".
2022-10-08gnu: pigx-sars-cov-2: Update to 0.0.8.Ricardo Wurmus
* 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.
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-23 05:29:45 +0000