diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 46 |
1 files changed, 31 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f6a37a4f8..4cd032abd4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8344,6 +8344,7 @@ paired-end data.") (sha256 (base32 "0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad")))) + (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9831,14 +9832,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.7") + (version "2.6.8") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f")))) + "0gijx2l2y00h6gfj3gfr7rd4vva6qf2vkfdfy5gdmvqlxy84ka38")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10157,14 +10158,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips")))) + "01lf74pby7si2g3kgc10qzr6lkcbigqcgqs2j3anc38vzxv0zhwv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -12038,6 +12039,23 @@ graphs. This library makes it easy to work with @file{.loom} files for single-cell RNA-seq data.") (license license:bsd-3))) +;; pigx-scrnaseq does not work with the latest version of loompy. +(define-public python-loompy-for-pigx-scrnaseq + (package (inherit python-loompy) + (name "python-loompy") + (version "2.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/linnarsson-lab/loompy.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0pjyl532pl8sbv71yci6h0agchn0naw2qjcwj50n6afrsahbsag3")))) + ;; There are none. + (arguments '(#:tests? #f)))) + ;; We cannot use the latest commit because it requires Java 9. (define-public java-forester (let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6") @@ -12651,7 +12669,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.31") + (version "0.0.40") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12659,7 +12677,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0l3vd9xwqzap3mmyj8xwqp84kj7scbq308diqnwg2albphl75xqs")))) + "0y9x62cfwzhsp82imnawyamxp58bcb00yjxdy44spylqnjdlsaj8")))) (build-system gnu-build-system) ;; parts of the tests rely on access to the network (arguments '(#:tests? #f)) @@ -12808,7 +12826,7 @@ methylation and segmentation.") ("python-pandas" ,python-pandas) ("python-magic" ,python-magic) ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy) + ("python-loompy" ,python-loompy-for-pigx-scrnaseq) ("ghc-pandoc" ,ghc-pandoc) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc) ("samtools" ,samtools) @@ -13301,9 +13319,6 @@ in RNA-seq data.") (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") - ;; TODO: No module named 'louvain' - (delete-file "scanpy/tests/test_rank_genes_groups_logreg.py") - ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") (delete-file "scanpy/tests/test_preprocessing.py") @@ -13316,18 +13331,19 @@ in RNA-seq data.") #t))))) (propagated-inputs `(("python-anndata" ,python-anndata) + ("python-h5py" ,python-h5py) ("python-igraph" ,python-igraph) - ("python-numba" ,python-numba) ("python-joblib" ,python-joblib) + ("python-louvain" ,python-louvain) + ("python-matplotlib" ,python-matplotlib) ("python-natsort" ,python-natsort) ("python-networkx" ,python-networkx) - ("python-statsmodels" ,python-statsmodels) - ("python-scikit-learn" ,python-scikit-learn) - ("python-matplotlib" ,python-matplotlib) + ("python-numba" ,python-numba) ("python-pandas" ,python-pandas) + ("python-scikit-learn" ,python-scikit-learn) ("python-scipy" ,python-scipy) ("python-seaborn" ,python-seaborn) - ("python-h5py" ,python-h5py) + ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables))) (native-inputs `(("python-pytest" ,python-pytest))) |