diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 150 |
1 files changed, 103 insertions, 47 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02cafb2358..d6db02188f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12,6 +12,7 @@ ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -612,16 +613,22 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-pybedtools (package (name "python-pybedtools") - (version "0.7.10") + (version "0.8.0") (source (origin (method url-fetch) (uri (pypi-uri "pybedtools" version)) (sha256 (base32 - "0l2b2wrnj85azfqgr0zwr60f7j58vlla1hcgxvr9rwikpl8j72ji")))) + "1xl454ijvd4dzfvqgfahad49b49j7qy710fq9xh1rvk42z6x5ssf")))) (build-system python-build-system) (arguments - `(#:phases + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build python-build-system)) + ;; See https://github.com/daler/pybedtools/issues/192 + #:phases (modify-phases %standard-phases ;; See https://github.com/daler/pybedtools/issues/261 (add-after 'unpack 'disable-broken-tests @@ -631,21 +638,59 @@ intended to behave exactly the same as the original BWK awk.") (substitute* "pybedtools/test/test_scripts.py" (("def test_venn_mpl") "def _do_not_test_venn_mpl")) - ;; Requires internet access. (substitute* "pybedtools/test/test_helpers.py" + ;; Requires internet access. (("def test_chromsizes") - "def _do_not_test_chromsizes")) - ;; FIXME: these two fail for no good reason. - (substitute* "pybedtools/test/test1.py" - (("def test_issue_157") - "def _do_not_test_issue_157") - (("def test_to_dataframe") - "def _do_not_test_to_dataframe")) - #t))))) - (propagated-inputs - ;; Tests don't pass with Bedtools 2.27.1. - ;; See https://github.com/daler/pybedtools/issues/260 - `(("bedtools" ,bedtools-2.26) + "def _do_not_test_chromsizes") + ;; Broken as a result of the workaround used in the check phase + ;; (see: https://github.com/daler/pybedtools/issues/192). + (("def test_getting_example_beds") + "def _do_not_test_getting_example_beds")) + #t)) + ;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM. + ;; build system. + ;; Force the Cythonization of C++ files to guard against compilation + ;; problems. + (add-after 'unpack 'remove-cython-generated-files + (lambda _ + (let ((cython-sources (map (cut string-drop-right <> 4) + (find-files "." "\\.pyx$"))) + (c/c++-files (find-files "." "\\.(c|cpp|cxx)$"))) + (define (strip-extension filename) + (string-take filename (string-index-right filename #\.))) + (define (cythonized? c/c++-file) + (member (strip-extension c/c++-file) cython-sources)) + (for-each delete-file (filter cythonized? c/c++-files)) + #t))) + (add-after 'remove-cython-generated-files 'generate-cython-extensions + (lambda _ + (invoke "python" "setup.py" "cythonize"))) + (replace 'check + (lambda _ + (let* ((cwd (getcwd)) + (build-root-directory (string-append cwd "/build/")) + (build (string-append + build-root-directory + (find (cut string-prefix? "lib" <>) + (scandir (string-append + build-root-directory))))) + (scripts (string-append + build-root-directory + (find (cut string-prefix? "scripts" <>) + (scandir build-root-directory))))) + (setenv "PYTHONPATH" + (string-append build ":" (getenv "PYTHONPATH"))) + ;; Executable scripts such as 'intron_exon_reads.py' must be + ;; available in the PATH. + (setenv "PATH" + (string-append scripts ":" (getenv "PATH")))) + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively "pybedtools/test" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest"))))))) + (propagated-inputs + `(("bedtools" ,bedtools) ("samtools" ,samtools) ("python-matplotlib" ,python-matplotlib) ("python-pysam" ,python-pysam) @@ -654,9 +699,11 @@ intended to behave exactly the same as the original BWK awk.") `(("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-cython" ,python-cython) - ("python-nose" ,python-nose) - ("kentutils" ,kentutils) ; for bedGraphToBigWig - ("python-six" ,python-six))) + ("kentutils" ,kentutils) ; for bedGraphToBigWig + ("python-six" ,python-six) + ;; For the test suite. + ("python-pytest" ,python-pytest) + ("python-psutil" ,python-psutil))) (home-page "https://pythonhosted.org/pybedtools/") (synopsis "Python wrapper for BEDtools programs") (description @@ -667,34 +714,7 @@ Python.") (license license:gpl2+))) (define-public python2-pybedtools - (let ((pkg (package-with-python2 python-pybedtools))) - (package (inherit pkg) - (arguments - `(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) - (guix build utils) - (guix build python-build-system)) - ;; See https://github.com/daler/pybedtools/issues/192 - ,@(substitute-keyword-arguments (package-arguments pkg) - ((#:phases phases) - `(modify-phases ,phases - (replace 'check - (lambda _ - (let ((cwd (getcwd))) - (setenv "PYTHONPATH" - (string-append cwd "/build/" - (find (cut string-prefix? "lib" <>) - (scandir (string-append cwd "/build"))) - ":" (getenv "PYTHONPATH")))) - ;; The tests need to be run from elsewhere... - (mkdir-p "/tmp/test") - (copy-recursively "pybedtools/test" "/tmp/test") - (with-directory-excursion "/tmp/test" - (invoke "nosetests" - ;; This test fails for unknown reasons - "--exclude=.*test_getting_example_beds")) - #t)))))))))) + (package-with-python2 python-pybedtools)) (define-public python-biom-format (package @@ -14441,3 +14461,39 @@ Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs (Single nucleotide polymorphisms) and indels with respect to a reference genome and more.") (license license:expat)))) + +(define-public cnvkit + (package + (name "cnvkit") + (version "0.9.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/etal/cnvkit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) + (build-system python-build-system) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-future" ,python-future) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-reportlab" ,python-reportlab) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-pyfaidx" ,python-pyfaidx) + ("python-scipy" ,python-scipy) + ;; R packages + ("r-dnacopy" ,r-dnacopy))) + (home-page "https://cnvkit.readthedocs.org/") + (synopsis "Copy number variant detection from targeted DNA sequencing") + (description + "CNVkit is a Python library and command-line software toolkit to infer +and visualize copy number from high-throughput DNA sequencing data. It is +designed for use with hybrid capture, including both whole-exome and custom +target panels, and short-read sequencing platforms such as Illumina and Ion +Torrent.") + (license license:asl2.0))) |