| Age | Commit message (Expand) | Author |
|---|
| 2022-12-18 | gnu: python-scanpy: Use pyproject-build-system....* 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.
| Ricardo Wurmus |
| 2022-12-18 | gnu: python-multivelo: Simplify with pyproject-build-system....* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use
pyproject-build-system.
[arguments]: Remove custom 'build and 'install phases.
| Ricardo Wurmus |
| 2022-12-14 | gnu: bedtools-2.18: Use gexp....* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp.
[native-inputs]: Drop package label.
| Ricardo Wurmus |
| 2022-12-13 | gnu: bedops: Update to 2.4.41....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: tophat: Remove trailing #T from build phases and snippet....* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from
snippet.
[arguments]: Remove trailing #T from build phases.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-bx-python: Update to 0.9.0....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: bioawk: Use gexp....* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify
'install phase.
| Ricardo Wurmus |
| 2022-12-13 | gnu: blasr-libcpp: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove
trailing #T from build phases.
| Ricardo Wurmus |
| 2022-12-13 | gnu: pbbam: Drop input labels....* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
| Ricardo Wurmus |
| 2022-12-13 | gnu: pbbam: Update to 2.1.0....* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
| Ricardo Wurmus |
| 2022-12-13 | gnu: pbcopper: Update to 2.0.0....* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
| Ricardo Wurmus |
| 2022-12-13 | gnu: bedtools: Remove unnecessary quasiquotation....* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote.
[native-inputs]: Drop input label.
| Ricardo Wurmus |
| 2022-12-13 | gnu: bamutils: Update to 1.0.15....* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15.
[arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags.
[native-inputs]: Update libstatgen.
| Ricardo Wurmus |
| 2022-12-13 | gnu: bamtools: Update to 2.5.2....* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2.
[arguments]: Enable tests; remove extra phases.
[inputs]: Add jsoncpp.
[native-inputs]: Add pkg-config.
| Ricardo Wurmus |
| 2022-12-13 | gnu: aragorn: Update to 1.2.41....* 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+.
| Ricardo Wurmus |
| 2022-12-13 | gnu: cnvkit: Update to 0.9.9....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: seqmagick: Update to 0.8.4....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-cgatcore: Update to 0.6.14....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-dna-features-viewer: Update to 3.1.1....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-hicexplorer: Update to 3.7.2....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-pygenometracks: Update to 3.5....* 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.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-hicmatrix: Update to 16....* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 16.
[build-system]: Use pyproject-build-system.
[arguments]: Shuffle the quote.
| Ricardo Wurmus |
| 2022-12-13 | gnu: python-biopython: Update to 1.80....* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.80.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
| Ricardo Wurmus |
| 2022-12-12 | gnu: bioperl-minimal: Remove trailing #T from build phase....* gnu/packages/bioinformatics.scm (bioperl-minimal)[arguments]: Remove
trailing #T from build phase.
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-biom-format: Update to 2.1.12....* 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.
| Ricardo Wurmus |
| 2022-12-02 | gnu: Add python-scikit-bio....* gnu/packages/bioinformatics.scm (python-scikit-bio): New variable.
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-pairtools: Update to 1.0.2....* 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.
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-pairtools: Run tests conditionally....* gnu/packages/bioinformatics.scm (python-pairtools)[arguments]: Run tests
conditionally.
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-pybedtools: Use pyproject-build-system....* gnu/packages/bioinformatics.scm (python-pybedtools)[build-system]: Use
pyproject-build-system.
[arguments]: Import (guix build pyproject-build-system).
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-htsget: Update to 0.2.6....* gnu/packages/bioinformatics.scm (python-htsget): Update to 0.2.6.
[build-system]: Use pyproject-build-system.
| Ricardo Wurmus |
| 2022-12-02 | gnu: python-cellbender: Update to 0.2.2....* gnu/packages/bioinformatics.scm (python-cellbender): Update to 0.2.2.
[build-system]: Use pyproject-build-system.
| Ricardo Wurmus |
| 2022-12-02 | gnu: Add python-fanc....* gnu/packages/bioinformatics.scm (python-fanc): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
| Ricardo Wurmus |
| 2022-12-02 | gnu: Add python-genomic-regions....* gnu/packages/bioinformatics.scm (python-genomic-regions): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
| Ricardo Wurmus |
| 2022-11-25 | gnu: Add r-btools....* gnu/packages/bioinformatics.scm (r-btools): New variable.
| Navid Afkhami |
| 2022-11-17 | gnu: r-circus: Update to 0.1.7....* 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.
| Ricardo Wurmus |
| 2022-11-15 | gnu: Add r-disgenet2r....* gnu/packages/bioinformatics.scm (r-disgenet2r): New variable.
| Ricardo Wurmus |
| 2022-11-09 | gnu: Add r-pando....* gnu/packages/bioinformatics.scm (r-pando): New variable.
| Mădălin Ionel Patrașcu |
| 2022-11-04 | gnu: Add python-cooltools....* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
| Mădălin Ionel Patrașcu |
| 2022-11-04 | gnu: Add python-bioframe.... X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
| Mădălin Ionel Patrașcu |
| 2022-11-04 | gnu: r-dyngen: Update to 1.0.5....* gnu/packages/bioinformatics.scm (r-dyngen): Update to 1.0.5.
| Ricardo Wurmus |
| 2022-10-31 | gnu: 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 |
| 2022-10-28 | gnu: 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 |
| 2022-10-28 | gnu: flair: Set R_HOME....* gnu/packages/bioinformatics.scm (flair)[arguments]: Set R_HOME.
| Ricardo Wurmus |
| 2022-10-28 | gnu: flair: Add missing R package....* gnu/packages/bioinformatics.scm (flair)[inputs]: Add r-apeglm.
| Ricardo Wurmus |
| 2022-10-27 | gnu: 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 |
| 2022-10-27 | gnu: Add python-multivelo....* gnu/packages/bioinformatics.scm (python-multivelo): New variable.
| Mădălin Ionel Patrașcu |
| 2022-10-27 | gnu: Add r-seuratwrappers....* gnu/packages/bioinformatics.scm (r-seuratwrappers): New variable.
| Hong.Li@mdc-berlin.de |
| 2022-10-24 | gnu: 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 |
| 2022-10-23 | gnu: 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 |
| 2022-10-08 | gnu: 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 |
