diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 | ||||
| -rw-r--r-- | gnu/packages/python.scm | 38 |
2 files changed, 38 insertions, 38 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f8ce22a8b..45ab9aa7b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -838,6 +838,44 @@ well as many of the command line options.") multiple sequence alignments.") (license license:expat))) +(define-public python-pysam + (package + (name "python-pysam") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-" + version ".tar.gz")) + (sha256 + (base32 + "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; tests are excluded in the manifest + #:phases + (alist-cons-before + 'build 'set-flags + (lambda _ + (setenv "LDFLAGS" "-lncurses") + (setenv "CFLAGS" "-D_CURSES_LIB=1")) + %standard-phases))) + (inputs + `(("python-cython" ,python-cython) + ("python-setuptools" ,python-setuptools) + ("ncurses" ,ncurses) + ("zlib" ,zlib))) + (home-page "https://github.com/pysam-developers/pysam") + (synopsis "Python bindings to the SAMtools C API") + (description + "Pysam is a Python module for reading and manipulating files in the +SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It +also includes an interface for tabix.") + (license license:expat))) + +(define-public python2-pysam + (package-with-python2 python-pysam)) + (define-public clipper (package (name "clipper") diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4f34537df6..131ec6207b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1040,44 +1040,6 @@ get the local timezone information, unless you know the zoneinfo name, and under several distributions that's hard or impossible to figure out.") (license cc0))) -(define-public python-pysam - (package - (name "python-pysam") - (version "0.8.1") - (source - (origin - (method url-fetch) - (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-" - version ".tar.gz")) - (sha256 - (base32 - "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; tests are excluded in the manifest - #:phases - (alist-cons-before - 'build 'set-flags - (lambda _ - (setenv "LDFLAGS" "-lncurses") - (setenv "CFLAGS" "-D_CURSES_LIB=1")) - %standard-phases))) - (inputs - `(("python-cython" ,python-cython) - ("python-setuptools" ,python-setuptools) - ("ncurses" ,ncurses) - ("zlib" ,zlib))) - (home-page "https://github.com/pysam-developers/pysam") - (synopsis "Python bindings to the SAMtools C API") - (description - "Pysam is a Python module for reading and manipulating files in the -SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It -also includes an interface for tabix.") - (license license:expat))) - -(define-public python2-pysam - (package-with-python2 python-pysam)) - (define-public python2-pysqlite (package (name "python2-pysqlite") |