Age | Commit message (Collapse) | Author |
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* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
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* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
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* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
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* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
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* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
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* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
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* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
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* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
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* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
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* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
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* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
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* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
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* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
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* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
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* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
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* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
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* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
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* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
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* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
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* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
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* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
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* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
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The previous version has disappeared upstream.
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
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* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
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* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
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* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
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* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
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Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.
* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
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* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
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* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
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* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
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