| Age | Commit message (Expand) | Author |
|---|
| 2023-01-04 | gnu: bamtools: Build shared libraries.•••* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared
libraries instead of static libs.
| Ricardo Wurmus |
| 2023-01-04 | gnu: Add scallop.•••* gnu/packages/bioinformatics.scm (scallop): New variable.
| Ricardo Wurmus |
| 2023-01-03 | gnu: Add python-bcbio-gff.•••* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
| Ricardo Wurmus |
| 2022-12-30 | gnu: Add r-domultibarheatmap.•••* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
| Ricardo Wurmus |
| 2022-12-28 | gnu: r-giotto: Update to 1.1.2-1.3c8067c.•••* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
| Ricardo Wurmus |
| 2022-12-22 | gnu: Add r-bedtorch.•••* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
| Ricardo Wurmus |
| 2022-12-22 | gnu: Add r-rhtslib12.•••* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
| Ricardo Wurmus |
| 2022-12-22 | gnu: Add wiggletools.•••* gnu/packages/bioinformatics.scm (wiggletools): New variable.
| Ricardo Wurmus |
| 2022-12-22 | gnu: Add python-episcanpy.•••* gnu/packages/bioinformatics.scm (python-episcanpy): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2022-12-22 | gnu: Add python-bamnostic.•••* gnu/packages/bioinformatics.scm (python-bamnostic): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2022-12-21 | gnu: Add vembrane.•••* gnu/packages/bioinformatics.scm (vembrane): New variable.
| Ricardo Wurmus |
| 2022-12-21 | gnu: python-plastid: Update to 0.6.0.•••* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0.
[source]: Fetch from git repository.
[build-system]: Use pyproject-build-system.
[arguments]: Enable tests; add build phases 'unpack-test-data and
'build-extensions.
[inputs]: Add openssl.
[native-inputs]: Add test data.
| Ricardo Wurmus |
| 2022-12-21 | gnu: python-pysam: Update to 0.20.0.•••* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0.
[build-system]: Use pyproject-build-system.
| Ricardo Wurmus |
| 2022-12-21 | gnu: htslib: Update to 1.16.•••* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
| Ricardo Wurmus |
| 2022-12-21 | gnu: pbbam: Use htslib 1.14.•••* gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib
with htslib-1.14.
| Ricardo Wurmus |
| 2022-12-21 | gnu: Add htslib-1.14.•••* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
| Ricardo Wurmus |
| 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 |
