diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 371 |
1 files changed, 332 insertions, 39 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8653bb8a4c..a63c52a79c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7273,6 +7273,228 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-gutils + (let ((commit "10e36c7b580aacb2d952140a3fdd82418aaddea6") + (revision "1")) + (package + (name "r-gutils") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/gUtils") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wq9kd1afzy7ii510r20c4n9fkykj6p15q5c85ws27h1q5w4ghxy")))) + (properties `((upstream-name . "gUtils"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-s4vectors + r-stringr)) + (home-page "https://github.com/mskilab/gUtils") + (synopsis "Additional capabilities and speed for GenomicRanges operations") + (description + "This is an R package providing additional capabilities and speed for +@code{GenomicRanges} operations.") + (license license:gpl2)))) + +(define-public r-bamutils + (let ((commit "639dba901f16944fa1b7a8d7048701ba86a2cdb8") + (revision "1")) + (package + (name "r-bamutils") + (version (git-version "0.0.0.9000" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/bamutils/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0qwby2v5rydnipvf1iv1wz9nf02yq98k0xbc4inf9mqc54jwacs0")))) + (properties `((upstream-name . "bamUtils"))) + (build-system r-build-system) + (propagated-inputs + (list r-abind + r-biocgenerics + r-data-table + r-genomicalignments + r-genomicranges + r-gutils + r-rsamtools + r-variantannotation)) + (home-page "https://github.com/mskilab/bamutils/") + (synopsis "Utility functions for manipulating BAMs") + (description "This package provides utility functions for manipulating +BAM files.") + (license license:gpl2)))) + +(define-public r-gtrack + (let ((commit "a694fa36cedafca2658da79fc8e5b673535b15e5") + (revision "1")) + (package + (name "r-gtrack") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/gTrack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "070qlrbqsbj9max2vx740zigqh0ymvnw2pm1ia5la3wb4dbfwh2b")))) + (properties `((upstream-name . "gTrack"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-genomeinfodb + r-genomicranges + r-gutils + r-iranges + r-matrix + r-rcolorbrewer + r-rcpp + r-rcurl + r-rtracklayer + r-s4vectors)) + (home-page "https://github.com/mskilab/gTrack/") + (synopsis "Plot tracks of complex genomic data across multiple genomic windows") + (description + "This package provides an object for plotting GRanges, RleList, UCSC +file formats, and ffTrack objects in multi-track panels.") + (license license:gpl2)))) + +(define-public r-gchain + (let ((commit "dc393e8dd0d8efaf36270c04d7112db8553db36a") + (revision "1")) + (package + (name "r-gchain") + (version (git-version "0.2.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/gChain/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "105wgi5w2fhwq1grsvj6zjigwg0sny3z7zr577q8ki3qffjwdkj0")))) + (properties `((upstream-name . "gChain"))) + (build-system r-build-system) + (propagated-inputs + (list r-bamutils + r-biostrings + r-data-table + r-genomicalignments + r-genomicranges + r-gtrack + r-gutils + r-matrix + r-rtracklayer)) + (home-page "https://github.com/mskilab/gChain/") + (synopsis "Additional capabilities and speed for GenomicRanges operations") + (description + "This R package provides additional capabilities and speed for +GenomicRanges operations.") + (license license:gpl2)))) + +(define-public r-skitools + (let ((commit "22d107d32f063eb891eb5e7fb36996d1c0b0d2bc") + (revision "1")) + (package + (name "r-skitools") + (version (git-version "0.0.0.9000" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/skitools/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1977d9bkdk9l2n6niahfj9vksh9l1ga4g7c3b3x27lj1gc0qgr4z")))) + (properties `((upstream-name . "skitools"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-complexheatmap + r-data-table + r-devtools + r-dt + r-gchain + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gplots + r-gutils + r-htmlwidgets + r-hwriter + r-igraph + r-iranges + r-plotly + r-rcolorbrewer + r-reshape2 + r-s4vectors + r-stringr + r-variantannotation)) + (home-page "https://github.com/mskilab/skitools/") + (synopsis "Various mskilab R utilties") + (description + "This package provides R miscellaneous utilities for basic data +manipulation, debugging, visualization, lsf management, and common mskilab +tasks.") + (license license:expat)))) + +(define-public r-chromunity + (let ((commit "09fce8bc12cb84b45a6ea25bf8db6e5b75113d4f") + (revision "1")) + (package + (name "r-chromunity") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mskilab/chromunity") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0lp0h614k8fq6h9gpbylk4chh7q6w4qda8lx03ajrpppxmg7al2d")))) + (properties `((upstream-name . "chromunity"))) + (build-system r-build-system) + (propagated-inputs + (list r-arrow + r-biocgenerics + r-data-table + r-gchain + r-genomicranges + r-gutils + r-igraph + r-magrittr + r-mass + r-matrix + r-pbmcapply + r-plyr + r-r6 + r-skitools + r-zoo)) + (home-page "https://github.com/mskilab/chromunity") + (synopsis "Discovery of communities in Pore-C concatemers") + (description "This is a package for the discovery of communities in +Pore-C concatemers.") + (license license:gpl3)))) + (define-public r-presto (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad") (revision "0")) @@ -12514,6 +12736,12 @@ fasta subsequences.") (substitute* '("requirements.txt" "cooler.egg-info/requires.txt") (("cytoolz.*<.*0.11") "cytoolz")))) + ;; This version of flake8 just won't work with this version of + ;; pytest, because of dependency pinning. + (add-after 'unpack 'do-not-use-flake8 + (lambda _ + (substitute* "setup.cfg" + (("addopts = --flake8") "addopts = ")))) (add-after 'unpack 'patch-tests (lambda _ (substitute* "tests/test_create.py" @@ -12522,10 +12750,13 @@ fasta subsequences.") "access to genome.ucsc.edu\")\n" "def test_roundtrip"))) (substitute* "tests/test_util.py" - (("def test_fetch_chromsizes") - (string-append "@pytest.mark.skip(reason=\"requires network " - "access to genome.ucsc.edu\")\n" - "def test_fetch_chromsizes"))) + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes")) + ;; See https://github.com/open2c/cooler/issues/287 + (("skipif\\(six.PY2, reason=\"Scipy on Py2 is too old\"") + "skip(reason=\"Scipy is too new\"")) ;; This test depends on ipytree, which contains a lot of minified ;; JavaScript. (substitute* "tests/test_fileops.py" @@ -15541,47 +15772,49 @@ for the analysis and visualization of raw nanopore signal.") (license license:mpl2.0))) (define-public python-pyvcf - (package - (name "python-pyvcf") - (version "0.6.8") - ;; Use git, because the PyPI tarballs lack test data. - (source - (origin - (method git-fetch) - (uri (git-reference + (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9") + (revision "0")) + (package + (name "python-pyvcf") + (version (git-version "0.6.8" revision commit)) + ;; Use git, because the PyPI tarballs lack test data. + (source + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/jamescasbon/PyVCF.git") ;; Latest release is not tagged. - (commit "bfcedb9bad1a14074ac4526ffdb610611e073810"))) - (file-name (git-file-name name version)) - (sha256 + (commit commit))) + (file-name (git-file-name name version)) + (sha256 (base32 - "0c7lsssns3zp8fh2ibllzzra003srg9vbxqzmq6654akbzdb7lrf")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-sample-script - (lambda _ - ;; Add Python 3 compatibility to this sample script. - (substitute* "scripts/vcf_sample_filter.py" - (("print (.*)\n" _ arg) - (string-append "print(" arg ")\n"))))) - (add-after 'install 'remove-installed-tests - ;; Do not install test files. - (lambda* (#:key inputs outputs #:allow-other-keys) - (delete-file-recursively (string-append + "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-sample-script + (lambda _ + ;; Add Python 3 compatibility to this sample script. + (substitute* "scripts/vcf_sample_filter.py" + (("print (.*)\n" _ arg) + (string-append "print(" arg ")\n"))))) + (add-after 'install 'remove-installed-tests + ;; Do not install test files. + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file-recursively (string-append (site-packages inputs outputs) "/vcf/test"))))))) - (native-inputs - ;; Older setuptools is needed for use_2to3. - (list python-cython python-setuptools)) - (propagated-inputs - (list python-pysam python-rpy2)) - (home-page "https://github.com/jamescasbon/PyVCF") - (synopsis "Variant Call Format parser for Python") - (description "This package provides a @acronym{VCF,Variant Call Format} + (native-inputs + ;; Older setuptools is needed for use_2to3. + (list python-cython python-setuptools-for-tensorflow)) + (propagated-inputs + (list python-pysam python-rpy2)) + (home-page "https://github.com/jamescasbon/PyVCF") + (synopsis "Variant Call Format parser for Python") + (description "This package provides a @acronym{VCF,Variant Call Format} parser for Python.") - (license license:expat))) + (license license:expat)))) (define-public nanosv (package @@ -15996,6 +16229,43 @@ BigWig files, as well as efficient region coverage summary over intervals from both types of files.") (license license:expat))) +(define-public mudskipper + (package + (name "mudskipper") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (crate-uri "mudskipper" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #false ;fail because the "mudskipper" crate cannot be found + #:cargo-inputs + (("rust-bio" ,rust-bio-0.39) + ("rust-bio-types" ,rust-bio-types-0.12) + ("rust-clap" ,rust-clap-2) + ("rust-coitrees" ,rust-coitrees-0.2) + ("rust-env-logger" ,rust-env-logger-0.9) + ("rust-fnv" ,rust-fnv-1) + ("rust-indicatif" ,rust-indicatif-0.16) + ("rust-libradicl" ,rust-libradicl-0.4) + ("rust-linecount" ,rust-linecount-0.1) + ("rust-log" ,rust-log-0.4) + ("rust-num-cpus" ,rust-num-cpus-1) + ("rust-rust-htslib" ,rust-rust-htslib-0.38)))) + (native-inputs + (list cmake pkg-config)) + (inputs + (list zlib xz)) + (home-page "https://github.com/OceanGenomics/mudskipper") + (synopsis "Convert genomic alignments to transcriptomic BAM/RAD files.") + (description "Mudskipper is a tool for projecting genomic alignments to +transcriptomic coordinates.") + (license license:bsd-3))) + (define-public r-ascat (package (name "r-ascat") @@ -16155,6 +16425,29 @@ integration, exploration, and analysis of high-dimensional single-cell cytometry and imaging data.") (license license:expat)))) +(define-public r-compgenomrdata + (let ((commit "24484cb77631e1123ead6c329b9d62c160e600c6") + (revision "1")) + (package + (name "r-compgenomrdata") + (version (git-version "0.1.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/compgenomr/compGenomRData") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06gdvz4m4qlb1ylv10qfx09zv4c95cm7nps4y2s67m946kv8czv8")))) + (properties `((upstream-name . "compGenomRData"))) + (build-system r-build-system) + (home-page "https://github.com/compgenomr/compGenomRData") + (synopsis "Data for Computational Genomics with R book") + (description "This package provides data for the book \"Computational +Genomics with R\".") + (license license:gpl3)))) + (define-public r-cytonorm (let ((commit "e4b9d343ee65db3c422800f1db3e77c25abde987") (revision "1")) |