| Age | Commit message (Expand) | Author |
|---|
| 2023-02-07 | gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-02-07 | Revert "gnu: Add bitmapperbs."...This reverts commit f55cc9cb0fb6c5dd56196009681e042c1aef415d.
This commit was prematurely pushed.
| Ricardo Wurmus |
| 2023-02-07 | gnu: Add bitmapperbs....* gnu/packages/bioinformatics.scm (bitmapperbs): New variable.
| Navid Afkhami |
| 2023-02-06 | gnu: Add r-ggsankey....* gnu/packages/bioinformatics.scm (r-ggsankey): New variable.
| Ricardo Wurmus |
| 2023-02-03 | gnu: Add r-psupertime....* gnu/packages/bioinformatics.scm (r-psupertime): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-02-03 | gnu: Add python-demuxem....* gnu/packages/bioinformatics.scm (python-demuxem): New variable.
| Navid Afkhami |
| 2023-02-03 | gnu: Add python-pegasusio....* gnu/packages/bioinformatics.scm (python-pegasusio): New variable.
| Navid Afkhami |
| 2023-02-03 | gnu: Add r-streamgraph....* gnu/packages/bioinformatics.scm (r-streamgraph): New variable.
| Navid Afkhami |
| 2023-01-25 | gnu: gdcm: Add documentation....* gnu/packages/bioinformatics.scm (gdcm)[outputs]: New field.
[arguments]: Add #:phases. Augment #:configure-flags.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Tor-björn Claesson |
| 2023-01-25 | gnu: gdcm: Ignore 3 failing tests....* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Skip three more
failing tests.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Tor-björn Claesson |
| 2023-01-25 | gnu: Add python-slamdunk....* gnu/packages/bioinformatics.scm (python-slamdunk): New variable.
| Ricardo Wurmus |
| 2023-01-25 | gnu: Add python-phylophlan....* gnu/packages/bioinformatics.scm (python-phylophlan): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
| Mădălin Ionel Patrașcu |
| 2023-01-25 | gnu: Add python-hclust2....* gnu/packages/bioinformatics.scm (python-hclust2): New variable.
| Mădălin Ionel Patrașcu |
| 2023-01-25 | gnu: Add python-cmseq....* gnu/packages/bioinformatics.scm (python-cmseq): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
| Mădălin Ionel Patrașcu |
| 2023-01-25 | gnu: Add python-bcbio-gff/biopython-1.73....* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): New variable.
| Ricardo Wurmus |
| 2023-01-20 | gnu: Add r-tsis....* gnu/packages/bioinformatics.scm (r-tsis): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-01-20 | gnu: Add r-doubletcollection....* gnu/packages/bioinformatics.scm (r-doubletcollection): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-01-20 | gnu: Add python-vireosnp....* gnu/packages/bioinformatics.scm (python-vireosnp): New variable.
| Simon Tournier |
| 2023-01-15 | gnu: gdcm: Fix recursive Git source hash....The hash being used covered only the gdcm repository, not the gdcmdata
submodule.
* gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash.
Reported by civodul in #guix.
| Tobias Geerinckx-Rice |
| 2023-01-17 | gnu: gdcm: Update to 3.0.20....* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20.
[home-page, license]: Update.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Tor-björn Claesson |
| 2023-01-16 | gnu: r-cytonorm: Update to 0.0.10-1.166f9ff....* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
| Ricardo Wurmus |
| 2023-01-13 | gnu: r-signac: Update to 1.9.0-1.af41427....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427.
[propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa,
r-qlcmatrix, and r-seurat; add r-vctrs.
| Ricardo Wurmus |
| 2023-01-13 | gnu: python-cellbender: Update source hash....The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52
to d92cfc5a55c8b1771348468035993c52df975170.
* gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
| Marius Bakke |
| 2023-01-12 | gnu: Add cellsnp-lite....* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
| Simon Tournier |
| 2023-01-09 | gnu: Add r-gg3d....* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
| Ricardo Wurmus |
| 2023-01-08 | gnu: Move Java XML packages to new module....* gnu/packages/xml.scm (java-simple-xml, java-jaxp,
java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib,
java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2,
java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these
variables from here...
* gnu/packages/java-xml.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Register new file.
* gnu/packages/axoloti.scm,
gnu/packages/batik.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/groovy.scm,
gnu/packages/java.scm,
gnu/packages/maven.scm: Adjust module imports.
| Ricardo Wurmus |
| 2023-01-08 | gnu: Add gdcm....* gnu/packages/bioinformatics.scm (gdcm): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Antero Mejr |
| 2023-01-07 | gnu: Use old setuptools in packages that relies on use_2to3 conversion....This fixes a regression since 520cdf80581669646ff61e9f18f3b27045556e76 where
the use_2to3 functionality was removed from setuptools.
* gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from
PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57.
* gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]:
Likewise.
* gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add
PYTHON-SETUPTOOLS-57.
* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from
PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57.
| Marius Bakke |
| 2023-01-06 | gnu: bbmap: Update to 39.01....* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
| Ricardo Wurmus |
| 2023-01-06 | gnu: bbmap: Use gexp....* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
| Ricardo Wurmus |
| 2023-01-06 | gnu: nanopolish: Drop input labels....* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
| Ricardo Wurmus |
| 2023-01-06 | gnu: nanopolish: Update to 0.14.0....* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0.
[source]: Update snippet.
[arguments]: Use gexp; use cc-for-target; drop #T from build phases.
[inputs]: Add minimap2.
[native-inputs]: Add cmake-minimal.
| Ricardo Wurmus |
| 2023-01-06 | gnu: filtlong: Use Python 3....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with
python-wrapper.
| Ricardo Wurmus |
| 2023-01-06 | gnu: filtlong: Use gexp....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
| Ricardo Wurmus |
| 2023-01-06 | gnu: filtlong: Drop input labels....* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
| Ricardo Wurmus |
| 2023-01-06 | gnu: filtlong: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
| Ricardo Wurmus |
| 2023-01-06 | gnu: ngless: Use gexp....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
| Ricardo Wurmus |
| 2023-01-06 | gnu: ngless: Remove trailing #T from build phases....* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T.
| Ricardo Wurmus |
| 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 |
