diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 169 |
1 files changed, 156 insertions, 13 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e23bafa623..617908a4a6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> -;;; Copyright © 2016 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> @@ -2334,6 +2334,62 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.") files. The code was previously part of the cutadapt tool.") (license license:expat))) +(define-public python-deeptoolsintervals + (package + (name "python-deeptoolsintervals") + (version "0.1.9") + (source (origin + (method url-fetch) + (uri (pypi-uri "deeptoolsintervals" version)) + (sha256 + (base32 + "1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x")))) + (build-system python-build-system) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/deeptools/deeptools_intervals") + (synopsis "Create GTF-based interval trees with associated meta-data") + (description + "This package provides a Python module creating/accessing GTF-based +interval trees with associated meta-data. It is primarily used by the +@code{deeptools} package.") + (license license:expat))) + +(define-public python-deeptools + (package + (name "python-deeptools") + (version "3.4.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "deepTools" version)) + (sha256 + (base32 + "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + (build-system python-build-system) + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-numpydoc" ,python-numpydoc) + ("python-py2bit" ,python-py2bit) + ("python-pybigwig" ,python-pybigwig) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy) + ("python-deeptoolsintervals" ,python-deeptoolsintervals) + ("python-plotly" ,python-plotly))) + (home-page "https://pypi.org/project/deepTools/") + (synopsis "Useful tools for exploring deep sequencing data") + (description "This package addresses the challenge of handling large amounts +of data that are now routinely generated from DNA sequencing centers. +@code{deepTools} contains useful modules to process the mapped reads data for +multiple quality checks, creating normalized coverage files in standard bedGraph +and bigWig file formats, that allow comparison between different files. Finally, +using such normalized and standardized files, deepTools can create many +publication-ready visualizations to identify enrichments and for functional +annotations of the genome.") + ;; The file deeptools/cm.py is licensed under the BSD license. The + ;; remainder of the code is licensed under the MIT license. + (license (list license:bsd-3 license:expat)))) + (define-public cutadapt (package (name "cutadapt") @@ -4886,14 +4942,24 @@ files and writing bioinformatics applications.") "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ; requires Python 2.7 + `(#:python ,python-2 ; requires Python 2.7 + #:tests? #f ; test data are not included + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-weave + (lambda _ + (substitute* "warpedlmm/util/linalg.py" + (("from scipy import linalg, weave") + "from scipy import linalg\nimport weave")) + #t))))) (propagated-inputs `(("python-scipy" ,python2-scipy) ("python-numpy" ,python2-numpy) ("python-matplotlib" ,python2-matplotlib) ("python-fastlmm" ,python2-fastlmm) ("python-pandas" ,python2-pandas) - ("python-pysnptools" ,python2-pysnptools))) + ("python-pysnptools" ,python2-pysnptools) + ("python-weave" ,python2-weave))) (native-inputs `(("python-mock" ,python2-mock) ("python-nose" ,python2-nose) @@ -9102,6 +9168,46 @@ samples into a single report. It contains modules for a large number of common bioinformatics tools.") (license license:gpl3+))) +(define-public variant-tools + (package + (name "variant-tools") + (version "3.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vatlab/varianttools.git") + ;; There is no tag corresponding to version 3.1.2 + (commit "813ae4a90d25b69abc8a40f4f70441fe09015249"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g")))) + (build-system python-build-system) + (inputs + `(("boost" ,boost) + ("c-blosc" ,c-blosc) + ("gsl" ,gsl) + ("hdf5" ,hdf5) + ("hdf5-blosc" ,hdf5-blosc) + ("python-cython" ,python-cython) + ("zlib" ,zlib))) + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-pycurl" ,python-pycurl) + ("python-pyzmq" ,python-pyzmq) + ("python-scipy" ,python-scipy) + ("python-tables" ,python-tables))) + (home-page "https://vatlab.github.io/vat-docs/") + (synopsis "Analyze genetic variants from Next-Gen sequencing studies") + (description + "Variant tools is a tool for the manipulation, annotation, +selection, simulation, and analysis of variants in the context of next-gen +sequencing analysis. Unlike some other tools used for next-gen sequencing +analysis, variant tools is project based and provides a whole set of tools to +manipulate and analyze genetic variants.") + (license license:gpl3+))) + (define-public r-chipseq (package (name "r-chipseq") @@ -9660,13 +9766,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.4") + (version "3.1.5") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0lhjbjhv1hnx5i3gkx41k68i8ykay3f24708h30wx9xywww9lsvi")))) + "1lbq2pqhb6ih6iqawlnzdh05zff71pwbw1cpfv2sld3pd7kz0zkm")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9688,7 +9794,6 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) - ("r-metap" ,r-metap) ("r-patchwork" ,r-patchwork) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) @@ -10634,14 +10739,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.14.3") + (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6")))) + "0ib0grhd9zbrn0dkrm4aa7qj7h0y6z1dvyx1ab3w6vczw7xghsfb")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -13152,7 +13257,7 @@ version does count multisplits.") (define-public minimap2 (package (name "minimap2") - (version "2.10") + (version "2.17") (source (origin (method url-fetch) @@ -13161,7 +13266,7 @@ version does count multisplits.") "minimap2-" version ".tar.bz2")) (sha256 (base32 - "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj")))) + "0hi7i9pzxhvjj44khzzzj1lrn5gb5837arr4wgln7k1k5n4ci2mn")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are none @@ -13208,6 +13313,42 @@ cases include: @end enumerate\n") (license license:expat))) +(define-public miniasm + (package + (name "miniasm") + (version "0.3") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/lh3/miniasm/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0g89pa98dvh34idv7w1zv12bsbyr3a11c4qb1cdcz68gyda88s4v")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "miniasm" bin) + (install-file "minidot" bin))))))) + (home-page "https://github.com/lh3/miniasm") + (synopsis "Ultrafast de novo assembly for long noisy reads") + (description "Miniasm is a very fast OLC-based de novo assembler for noisy +long reads. It takes all-vs-all read self-mappings (typically by minimap) as +input and outputs an assembly graph in the GFA format. Different from +mainstream assemblers, miniasm does not have a consensus step. It simply +concatenates pieces of read sequences to generate the final unitig sequences. +Thus the per-base error rate is similar to the raw input reads.") + (license license:expat))) + (define-public r-circus (package (name "r-circus") @@ -13366,14 +13507,14 @@ in RNA-seq data.") (define-public python-scanpy (package (name "python-scanpy") - (version "1.4.5.1") + (version "1.4.6") (source (origin (method url-fetch) (uri (pypi-uri "scanpy" version)) (sha256 (base32 - "14kh1ji70xxhmri5q8sgcibsidhr6f221wxrcw8a5xvibj5da17j")))) + "0s2b6cvaigx4wzw3850qb93sjwwxbzh22kpbp498zklc5rjpbz4l")))) (build-system python-build-system) (arguments `(#:phases @@ -13383,6 +13524,7 @@ in RNA-seq data.") ;; These tests require Internet access. (delete-file-recursively "scanpy/tests/notebooks") (delete-file "scanpy/tests/test_clustering.py") + (delete-file "scanpy/tests/test_datasets.py") ;; TODO: I can't get the plotting tests to work, even with Xvfb. (delete-file "scanpy/tests/test_plotting.py") @@ -13399,8 +13541,8 @@ in RNA-seq data.") ("python-h5py" ,python-h5py) ("python-igraph" ,python-igraph) ("python-joblib" ,python-joblib) - ("python-louvain" ,python-louvain) ("python-legacy-api-wrap" ,python-legacy-api-wrap) + ("python-louvain" ,python-louvain) ("python-matplotlib" ,python-matplotlib) ("python-natsort" ,python-natsort) ("python-networkx" ,python-networkx) @@ -13413,6 +13555,7 @@ in RNA-seq data.") ("python-seaborn" ,python-seaborn) ("python-statsmodels" ,python-statsmodels) ("python-tables" ,python-tables) + ("python-tqdm" ,python-tqdm) ("python-umap-learn" ,python-umap-learn))) (native-inputs `(("python-pytest" ,python-pytest) |