| Age | Commit message (Expand) | Author |
|---|
| 2022-04-06 | gnu: Add r-rnaseqdtu....* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Hong Li |
| 2022-04-05 | gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR....This is needed since the update of python-loompy.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename
'set-PYTHONPATH to 'set-additional-environment-variables and set
NUMBA_CACHE_DIR.
| Ricardo Wurmus |
| 2022-04-05 | gnu: pigx-scrnaseq: Use new inputs style....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
| Ricardo Wurmus |
| 2022-04-05 | gnu: pigx-scrnaseq: Update to 1.1.8....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8.
[patches]: Remove.
[native-inputs]: Remove.
* gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-04-04 | gnu: freebayes: Fix test suite....* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
| Efraim Flashner |
| 2022-04-04 | gnu: smithwaterman: Use new style for phases....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
| Efraim Flashner |
| 2022-04-04 | gnu: smithwaterman: Fix cross-compiling....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add
make-flag to use cxx-for-target. Adjust custom 'patch-source and
'build-dynamic phases to use cross toolchain binaries when cross
compiling. Remove trailing #t from phases.
| Efraim Flashner |
| 2022-03-31 | gnu: python-velocyto: Set cache directory for Numba....* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
| Ricardo Wurmus |
| 2022-03-31 | gnu: wfmash: Enable test suite....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable
tests. Add custom 'check phase based on upstream's own CI tests.
[native-inputs]: Add samtools.
| Efraim Flashner |
| 2022-03-31 | gnu: Add wfmash....* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-03-31 | gnu: htslib: Add bzip2 and xz to inputs....htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz
should be listed in inputs even though they are already present implicitly in
native-inputs. Else, cross-compilation will fail.
* gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Arun Isaac |
| 2022-03-31 | gnu: python-loompy: Update to 3.0.7....* gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7.
[arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir;
respect TESTS? argument in 'check phase.
[propagated-inputs]: Add python-click, python-numba, and
python-numpy-groupies.
| Ricardo Wurmus |
| 2022-03-29 | gnu: r-signac: Update to 1.6.0-2.458e647....* gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647.
[propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings,
r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2022-03-29 | gnu: plink-ng: Update to 2.00a3-20220315....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
| Ricardo Wurmus |
| 2022-03-29 | gnu: Add r-cytobackbone....* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2022-03-29 | gnu: pigx-sars-cov2-ww: Update to 0.0.5....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5.
[source]: Remove patch.
[arguments]: Disable tests.
* gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-03-29 | gnu: pigx-rnaseq: Update to 0.0.20....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20.
[source]: Remove patch.
[inputs]: Add megadepth.
* gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Ricardo Wurmus |
| 2022-03-09 | gnu: Add r-scopeloomr....* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
| Ricardo Wurmus |
| 2022-03-02 | gnu: texlive-latex-pgf: Rename to "texlive-pgf"....Suggested by Ricardo Wurmus.
* gnu/packages/tex.scm (texlive-latex-pgf): Rename to...
(texlive-pgf): ... this. Change 'name' accordingly.
(texlive-latex-pgf): Define as deprecated.
(texlive-beamer)[propagated-inputs]: Use the new name.
(texlive-todonotes)[propagated-inputs]: Likewise.
(texlive-adjustbox)[propagated-inputs]: Likewise.
(texlive-tcolorbox)[propagated-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Likewise.
| Ludovic Courtès |
| 2022-02-27 | gnu: minimap2: Update to 2.24....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
| Efraim Flashner |
| 2022-02-22 | gnu: Add r-dyngen....* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
| Ricardo Wurmus |
| 2022-02-15 | gnu: python-gffutils: Update to 0.10.1....* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase. Respect TESTS? in check phase while at
it.
| Marius Bakke |
| 2022-01-31 | gnu: Add scvelo....* gnu/packages/bioinformatics.scm (scvelo): New variable.
| Ricardo Wurmus |
| 2022-01-31 | gnu: python-louvain-0.6: Update to 0.7.1....* gnu/packages/graph.scm (python-louvain-0.6): Update to 0.7.1.
[arguments]: Add build phases 'find-igraph and 'pretend-version.
[native-inputs]: Add python-setuptools-scm and python-wheel.
Rename this variable...
(python-louvain-0.7): ...to this, naturally.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Update
reference to python-louvain-0.6.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Remove trailing #T from build phase....* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
| Ricardo Wurmus |
| 2022-01-31 | gnu: bwa-meth: Update to 0.2.3....* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-sars-cov2-ww: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww)[arguments]: Set
PYTHONPATH variable in new build phase.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-scrnaseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-bsseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[arguments]: Set PYTHONPATH
variable in new build phase.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-chipseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Set PYTHONPATH
variable in new build phase.
| Ricardo Wurmus |
| 2022-01-27 | gnu: pigx-rnaseq: Fix Python module capture....The build system expects all Python modules to be on PYTHONPATH.
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Set PYTHONPATH
variable in new build phase.
| Ricardo Wurmus |
| 2022-01-22 | gnu: cwltool: Update to 3.1.20220119140128....* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20220119140128.
[propagated-inputs]: Change from PYTHON-RDFLIB-5 to PYTHON-RDFLIB.
[native-inputs]: Remove PYTHON-RDFLIB-JSONLD.
| Marius Bakke |
| 2022-01-22 | gnu: python-pyvcf: Build with old setuptools....* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add
PYTHON-SETUPTOOLS.
| Marius Bakke |
| 2022-01-21 | gnu: Add r-scseqcomm....* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
| zimoun |
| 2022-01-21 | gnu: Add r-icellnet....* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
| zimoun |
| 2022-01-20 | gnu: samtools-0.1: Install headers and library....* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases
'install-library and 'install-headers.
| Ricardo Wurmus |
| 2022-01-20 | gnu: Add r-doubletfinder....* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
| Ricardo Wurmus |
| 2022-01-18 | gnu: python-rdflib: Update to 6.1.1....* gnu/packages/rdf.scm (python-rdflib): Update to 6.1.1.
[arguments]: Remove #:tests. Add #:phases.
[native-inputs]: Change from PYTHON-NOSE to PYTHON-PYTEST.
(python-rdflib-5): New variable.
(python2-rdflib): Inherit from PYTHON-RDFLIB-5.
* gnu/packages/python-xyz.scm (python-prov): Change from PYTHON-RDFLIB to
PYTHON-RDFLIB-5.
* gnu/packages/bioinformatics.scm (cwltool): Likewise.
| Marius Bakke |
| 2022-01-17 | Merge branch 'version-1.4.0'...With resolved conflicts in:
gnu/packages/gnome.scm
gnu/packages/openstack.scm
gnu/packages/python-xyz.scm
| Maxim Cournoyer |
| 2022-01-17 | gnu: sambamba: Update to 0.8.2....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.2.
[arguments]: Sett CC and D_LD in build phase.
[native-inputs]: Add ld-gold-wrapper and binutils-gold.
| Ricardo Wurmus |
| 2022-01-10 | gnu: clipper: Remove obsolete phase....* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| Sarah Morgensen |
| 2022-01-10 | gnu: python-biom-format: Remove obsolete phase....* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
| Sarah Morgensen |
| 2022-01-10 | gnu: python-pysam: Update to 0.18.0....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.18.0.
[source]: Add FIXME to clarify bundled libraries in use.
[phases]{check}: Streamline.
[propagated-inputs]: Use latest htslib (1.14).
[native-inputs]: Use latest samtools and bcftools (1.14). Remove python-nose.
| Maxim Cournoyer |
| 2022-01-10 | gnu: bcftools: Update to 1.14....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.14.
(bcftools-1.12): New variable.
(bcftools-1.10): Use package/inherit and delete trailing #t.
[name]: Delete field.
| Maxim Cournoyer |
| 2022-01-10 | gnu: samtools: Update to 1.14....* gnu/packages/bioinformatics.scm (samtools): Update to 1.14.
[modules]: Delete argument.
[phases]{install-library, install-headers}: Delete phases. This version no
longer includes the legacy library (it links to htslib directly).
(samtools-1.12): New variable.
| Maxim Cournoyer |
| 2022-01-10 | gnu: htslib: Update to 1.14....* gnu/packages/bioinformatics.scm (htslib): Update to 1.14.
(htslib-1.12): New variable.
(htslib-1.10, htslib-1.9, htslib-1.3)
(htslib-for-samtools-1.2): Normalize style.
| Maxim Cournoyer |
| 2022-01-11 | gnu: stringtie: Update to 2.2.0....* gnu/packages/bioinformatics.scm (stringtie): Update to 2.2.0.
[source]: Simplify snippet.
[arguments]: Add make-flags; update build phases.
[inputs]: Remove samtools-0.1; add bzip2, htslib-for-stringtie, and
libdeflate.
[license]: Change to Expat license.
| Ricardo Wurmus |
| 2022-01-11 | gnu: Add htslib-for-stringtie....* gnu/packages/bioinformatics.scm (htslib-for-stringtie): New variable.
* gnu/packages/patches/htslib-for-stringtie.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
| Ricardo Wurmus |
| 2022-01-04 | gnu: r-archr: Update to 1.0.1-1.92ab814....* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.1-1.92ab814.
| Ricardo Wurmus |
| 2021-12-30 | gnu: Remove trailing period from synopsis....* gnu/packages/anddroid.scm (android-liblog, git-repo)[synopsis]: Remove
trailing period.
* gnu/packages/audio.scm (audio-to-midi)[synopsis]: Likewise.
* gnu/packages/bioinformatics.scm (python-mygene, python-scanpy,
nanosv)[synopsis]: Likewise.
* gnu/packages/cran.scm (r-gsubfn)[synopsis]: Likewise.
* gnu/packages/crates-io.scm (rust-ascii-1, rust-bindgen-0.59,
rust-byte-unit-4, rust-clircle-0.3, rust-dashmap-4, rust-dhcp4r-0.2,
rust-fast-float-0.2, rust-fst-0.4, rust-futures-core-preview-0.3,
rust-http-types-2, rust-hyper-0.14, rust-indexmap-1,
rust-minimal-lexical-0.1, rust-oorandom-11.1, rust-runtime-raw-0.3,
rust-sharded-slab-0.1, rust-takeable-option-0.4, rust-tower-service-0.3,
rust-ttf-parser-0.12)[synopsis]: Likewise.
* gnu/packages/disk.scm (f3)[synopsis]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-scribble-mode, emacs-psession)[synopsis]:
Likewise.
* gnu/packages/golang.scm (go-github-com-kylelemons-godebug)[synopsis]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-fsnotify, ghc-libyaml, ghc-emojis,
ghc-regex-tdfa, ghc-th-lift-instances, ghc-commonmark-pandoc)[synopsis]:
Likewise.
* gnu/packages/java.scm (java-commons-jxpath, java-jakarta-regexp)[synopsis]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-cl-annot, sbcl-envy)[synopsis]: Likewise.
* gnu/packages/mail.scm (go-gitlab.com-shackra-goimapnotify)[synopsis]:
Likewise.
* gnu/packages/maven.scm (maven-wagon-http-shared,
maven-surefire-plugin)[synopsis]: Likewise.
* gnu/packages/perl.scm (perl-text-soundex)[synopsis]: Likewise.
* gnu/packages/python-check.scm (python-httmock)[synopsis]: Likewise.
* gnu/packages/python-web.scm (python-bottle)[synopsis]: Likewise.
* gnu/packages/python-xyz.scm (python-olefile, python-tokenize-rt,
python-pylzma)[synopsis]: Likewise.
* gnu/packages/tex.scm (texlive-docstrip)[synopsis]: Likewise.
| Vagrant Cascadian |
