| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (r-giotto): New variable.
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* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3.
[source]: Remove trailing #t.
[arguments]: Remove trailing #t from phases.
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* gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to
remove cythonized file.
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* gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here...
* gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here.
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* gnu/packages/bioinformatics.scm (r-copykat): New variable.
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The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences.
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More
closely match the 'ar' and 'ld' commands when substituting them.
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* gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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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.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list.
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* 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.
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* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python.
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* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list
of G-Expressions.
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* 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.
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* gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase
'set-numba-cache-dir.
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* 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.
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* gnu/packages/bioinformatics.scm (wfmash): New variable.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
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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>
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* 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.
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* 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>
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* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315.
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* gnu/packages/bioinformatics.scm (r-cytobackbone): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-scopeloomr): New variable.
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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.
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* gnu/packages/bioinformatics.scm (minimap2): Update to 2.24.
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* gnu/packages/bioinformatics.scm (r-dyngen): New variable.
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* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase. Respect TESTS? in check phase while at
it.
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* gnu/packages/bioinformatics.scm (scvelo): New variable.
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* 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.
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* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Remove trailing #T
from build phase.
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* gnu/packages/bioinformatics.scm (bwa-meth): Update to 0.2.3.
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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.
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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.
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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.
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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.
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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.
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* 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.
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* gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Add
PYTHON-SETUPTOOLS.
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* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
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* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
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* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add build phases
'install-library and 'install-headers.
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* gnu/packages/bioinformatics.scm (r-doubletfinder): New variable.
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* 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.
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With resolved conflicts in:
gnu/packages/gnome.scm
gnu/packages/openstack.scm
gnu/packages/python-xyz.scm
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* gnu/packages/bioinformatics.scm (clipper)[arguments]<#:phases>: Remove
'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
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* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]
<#:phases>: Remove 'make-files-writable phase.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
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* 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.
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* 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.
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* 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.
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