diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 306 |
1 files changed, 134 insertions, 172 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02cafb2358..5dc3945035 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 @@ -4345,130 +4365,6 @@ interrupted by stop codons. OrfM finds and prints these ORFs.") (home-page "https://github.com/wwood/OrfM") (license license:lgpl3+))) -(define-public pplacer - (let ((commit "807f6f3")) - (package - (name "pplacer") - ;; The commit should be updated with each version change. - (version "1.1.alpha19") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/matsen/pplacer.git") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn")))) - (build-system ocaml-build-system) - (arguments - `(#:ocaml ,ocaml-4.01 - #:findlib ,ocaml4.01-findlib - #:modules ((guix build ocaml-build-system) - (guix build utils) - (ice-9 ftw)) - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'replace-bundled-cddlib - (lambda* (#:key inputs #:allow-other-keys) - (let* ((cddlib-src (assoc-ref inputs "cddlib-src")) - (local-dir "cddlib_guix")) - (mkdir local-dir) - (with-directory-excursion local-dir - (invoke "tar" "xvf" cddlib-src)) - (let ((cddlib-src-folder - (string-append local-dir "/" - (list-ref (scandir local-dir) 2) - "/lib-src"))) - (for-each make-file-writable (find-files "cdd_src" ".*")) - (for-each - (lambda (file) - (copy-file file - (string-append "cdd_src/" (basename file)))) - (find-files cddlib-src-folder ".*[ch]$"))) - #t))) - (add-after 'unpack 'fix-makefile - (lambda _ - ;; Remove system calls to 'git'. - (substitute* "Makefile" - (("^DESCRIPT:=pplacer-.*") - (string-append - "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n"))) - (substitute* "myocamlbuild.ml" - (("git describe --tags --long .*\\\" with") - (string-append - "echo -n v" ,version "-" ,commit "\" with"))) - #t)) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (copy-recursively "bin" bin)) - #t))))) - (native-inputs - `(("zlib" ,zlib) - ("gsl" ,gsl) - ("ocaml-ounit" ,ocaml4.01-ounit) - ("ocaml-batteries" ,ocaml4.01-batteries) - ("ocaml-camlzip" ,ocaml4.01-camlzip) - ("ocaml-csv" ,ocaml4.01-csv) - ("ocaml-sqlite3" ,ocaml4.01-sqlite3) - ("ocaml-xmlm" ,ocaml4.01-xmlm) - ("ocaml-mcl" ,ocaml4.01-mcl) - ("ocaml-gsl" ,ocaml4.01-gsl) - ("cddlib-src" ,(package-source cddlib)))) - (propagated-inputs - `(("pplacer-scripts" ,pplacer-scripts))) - (synopsis "Phylogenetic placement of biological sequences") - (description - "Pplacer places query sequences on a fixed reference phylogenetic tree -to maximize phylogenetic likelihood or posterior probability according to a -reference alignment. Pplacer is designed to be fast, to give useful -information about uncertainty, and to offer advanced visualization and -downstream analysis.") - (home-page "http://matsen.fhcrc.org/pplacer") - (license license:gpl3)))) - -;; This package is installed alongside 'pplacer'. It is a separate package so -;; that it can use the python-build-system for the scripts that are -;; distributed alongside the main OCaml binaries. -(define pplacer-scripts - (package - (inherit pplacer) - (name "pplacer-scripts") - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'enter-scripts-dir - (lambda _ (chdir "scripts") #t)) - (replace 'check - (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t)) - (add-after 'install 'wrap-executables - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin:" - (assoc-ref inputs "infernal") "/bin"))) - (display path) - (wrap-program (string-append bin "/refpkg_align.py") - `("PATH" ":" prefix (,path)))) - (let ((path (string-append - (assoc-ref inputs "hmmer") "/bin"))) - (wrap-program (string-append bin "/hrefpkg_query.py") - `("PATH" ":" prefix (,path))))) - #t))))) - (inputs - `(("infernal" ,infernal) - ("hmmer" ,hmmer))) - (propagated-inputs - `(("python-biopython" ,python2-biopython) - ("taxtastic" ,taxtastic))) - (synopsis "Pplacer Python scripts"))) - (define-public python2-pbcore (package (name "python2-pbcore") @@ -11172,7 +11068,7 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (native-inputs `(("ldc" ,ldc) ("rdmd" ,rdmd) - ("python" ,python-minimal) + ("python" ,python) ("biod" ,(let ((commit "4f1a7d2fb7ef3dfe962aa357d672f354ebfbe42e")) (origin @@ -14441,3 +14337,69 @@ 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))) + +(define-public python-pyfit-sne + (package + (name "python-pyfit-sne") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/KlugerLab/pyFIt-SNE.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "13wh3qkzs56azmmgnxib6xfr29g7xh09sxylzjpni5j0pp0rc5qw")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numpy" ,python-numpy))) + (inputs + `(("fftw" ,fftw))) + (native-inputs + `(("python-cython" ,python-cython))) + (home-page "https://github.com/KlugerLab/pyFIt-SNE") + (synopsis "FFT-accelerated Interpolation-based t-SNE") + (description + "t-Stochastic Neighborhood Embedding (t-SNE) is a highly successful +method for dimensionality reduction and visualization of high dimensional +datasets. A popular implementation of t-SNE uses the Barnes-Hut algorithm to +approximate the gradient at each iteration of gradient descent. This package +is a Cython wrapper for FIt-SNE.") + (license license:bsd-4))) |