diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 160 |
1 files changed, 160 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9813d07e9c..e143fb2c55 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -30,13 +30,17 @@ #:use-module (gnu packages base) #:use-module (gnu packages compression) #:use-module (gnu packages java) + #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages popt) #:use-module (gnu packages python) + #:use-module (gnu packages statistics) + #:use-module (gnu packages swig) #:use-module (gnu packages tbb) #:use-module (gnu packages vim) + #:use-module (gnu packages xml) #:use-module (gnu packages zip)) (define-public bedops @@ -507,6 +511,57 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.") (license license:gpl3))) +(define-public grit + (package + (name "grit") + (version "2.0.2") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/nboley/grit/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (alist-cons-after + 'unpack 'generate-from-cython-sources + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Delete these C files to force fresh generation from pyx sources. + (delete-file "grit/sparsify_support_fns.c") + (delete-file "grit/call_peaks_support_fns.c") + (substitute* "setup.py" + (("Cython.Setup") "Cython.Build") + ;; Add numpy include path to fix compilation + (("pyx\", \\]") + (string-append "pyx\", ], include_dirs = ['" + (assoc-ref inputs "python-numpy") + "/lib/python2.7/site-packages/numpy/core/include/" + "']"))) #t) + %standard-phases))) + (inputs + `(("python-scipy" ,python2-scipy) + ("python-numpy" ,python2-numpy) + ("python-pysam" ,python2-pysam) + ("python-networkx" ,python2-networkx))) + (native-inputs + `(("python-cython" ,python2-cython) + ("python-setuptools" ,python2-setuptools))) + (home-page "http://grit-bio.org") + (synopsis "Tool for integrative analysis of RNA-seq type assays") + (description + "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify +full length transcript models. When none of these data sources are available, +GRIT can be run by providing a candidate set of TES or TSS sites. In +addition, GRIT can merge in reference junctions and gene boundaries. GRIT can +also be run in quantification mode, where it uses a provided GTF file and just +estimates transcript expression.") + (license license:gpl3+))) + (define-public hisat (package (name "hisat") @@ -1001,6 +1056,111 @@ sequences.") ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed. (license license:gpl3+))) +(define-public shogun + (package + (name "shogun") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (string-append + "ftp://shogun-toolbox.org/shogun/releases/" + (version-major+minor version) + "/sources/shogun-" version ".tar.bz2")) + (sha256 + (base32 + "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ;no check target + #:phases + (alist-cons-after + 'unpack 'delete-broken-symlinks + (lambda _ + (for-each delete-file '("applications/arts/data" + "applications/asp/data" + "applications/easysvm/data" + "applications/msplicer/data" + "applications/ocr/data" + "examples/documented/data" + "examples/documented/matlab_static" + "examples/documented/octave_static" + "examples/undocumented/data" + "examples/undocumented/matlab_static" + "examples/undocumented/octave_static" + "tests/integration/data" + "tests/integration/matlab_static" + "tests/integration/octave_static" + "tests/integration/python_modular/tests")) + #t) + (alist-cons-after + 'unpack 'change-R-target-path + (lambda* (#:key outputs #:allow-other-keys) + (substitute* '("src/interfaces/r_modular/CMakeLists.txt" + "src/interfaces/r_static/CMakeLists.txt" + "examples/undocumented/r_modular/CMakeLists.txt") + (("\\$\\{R_COMPONENT_LIB_PATH\\}") + (string-append (assoc-ref outputs "out") + "/lib/R/library/"))) + #t) + (alist-cons-after + 'unpack 'fix-octave-modules + (lambda* (#:key outputs #:allow-other-keys) + (substitute* '("src/interfaces/octave_modular/CMakeLists.txt" + "src/interfaces/octave_static/CMakeLists.txt") + (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) + + ;; change target directory + (substitute* "src/interfaces/octave_modular/CMakeLists.txt" + (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") + (string-append (assoc-ref outputs "out") + "/share/octave/packages"))) + #t) + (alist-cons-before + 'build 'set-HOME + ;; $HOME needs to be set at some point during the build phase + (lambda _ (setenv "HOME" "/tmp") #t) + %standard-phases)))) + #:configure-flags + (list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT + ;;"-DJavaModular=ON" ;requires unpackaged jblas + ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray + ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist + ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file + "-DOctaveModular=ON" + "-DOctaveStatic=ON" + "-DPythonModular=ON" + "-DPythonStatic=ON" + "-DRModular=ON" + "-DRStatic=ON" + "-DCmdLineStatic=ON"))) + (inputs + `(("python" ,python) + ("numpy" ,python-numpy) + ("r" ,r) + ("octave" ,octave) + ("swig" ,swig) + ("hdf5" ,hdf5) + ("atlas" ,atlas) + ("arpack" ,arpack-ng) + ("lapack" ,lapack) + ("glpk" ,glpk) + ("libxml2" ,libxml2) + ("lzo" ,lzo) + ("zlib" ,zlib))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://shogun-toolbox.org/") + (synopsis "Machine learning toolbox") + (description + "The Shogun Machine learning toolbox provides a wide range of unified and +efficient Machine Learning (ML) methods. The toolbox seamlessly allows to +combine multiple data representations, algorithm classes, and general purpose +tools. This enables both rapid prototyping of data pipelines and extensibility +in terms of new algorithms.") + (license license:gpl3+))) + (define-public vcftools (package (name "vcftools") |