diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 34 | ||||
| -rw-r--r-- | gn/packages/python.scm | 99 |
2 files changed, 111 insertions, 22 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2f755a6..b77ccb4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -178,7 +178,7 @@ ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-passlib" ,python2-passlib) - ("python2-piddle" ,python2-piddle) + ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) @@ -202,3 +202,35 @@ ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x + +(define-public genenetwork2-database-small + (let ((md5 "93e745e9c")) + (package + (name "genenetwork2-database-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") + (file-name (string-append name "-" md5)) + (sha256 + (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) + (build-system trivial-build-system) + (native-inputs `(("unzip" ,unzip) + ("source" ,source))) + + (arguments + `(#:modules ((guix build utils)) + #:builder (begin + (use-modules (guix build utils)) + (let ((source (assoc-ref %build-inputs "source")) + (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) + ) + (and (mkdir "db") + (zero? (system* unzip source "-d" "db")) + (chdir "db")))))) + (home-page "http://genenetwork.org/") + (synopsis "Small database to run on genenetwork") + (description "Genenetwork installation + database.") + (license license:agpl3+)))) + diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 8f2bc80..7781521 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -357,32 +357,89 @@ project)") (description #f) (license #f))) -(define-public python2-piddle +(define-public python2-pil-1.1.6 (package - (name "python2-piddle") - (version "1.0.15") + (name "python2-pil") + (version "1.1.6") (source - (origin - (method url-fetch) - (uri (string-append - ;; http://sourceforge.net/projects/numpy/files/Old%20Numarray/1.5.2/numarray-1.5.2.tar.gz/download - "mirror://sourceforge/piddle/piddle-" version ".zip" - )) - ;; (file-name (string-append name "-" version ".zip")) - (sha256 - (base32 - "0jaxfsrcgqb5cf2wznxnpdws5khlrdixmg85lrhq2zl9cy6dfdya")))) - (native-inputs - `(("unzip" ,unzip))) - + (origin + (method url-fetch) + (uri (string-append + "http://effbot.org/downloads/Imaging-" + version ".tar.gz")) + (sha256 + (base32 + "141zidl3s9v4vfi3nsbg42iq1lc2a932gprqr1kij5hrnn53bmvx")) + (modules '((guix build utils))) + (snippet + ;; Adapt to newer freetype. As the package is unmaintained upstream, + ;; there is no use in creating a patch and reporting it. + '(substitute* "_imagingft.c" + (("freetype/") + "freetype2/"))))) (build-system python-build-system) - ;; (native-inputs - ;; `(("python-setuptools" ,python-setuptools))) + (inputs + `(("freetype" ,freetype) + ("libjpeg" ,libjpeg) + ("libtiff" ,libtiff) + ("python-setuptools" ,python-setuptools) + ("zlib" ,zlib))) (arguments + ;; Only the fork python-pillow works with Python 3. `(#:python ,python-2 - #:tests? #f - )) ; no 'setup.py test' really! - (home-page "http://www.numpy.org/") + #:tests? #f ; no check target + #:phases + (alist-cons-before + 'build 'configure + ;; According to README and setup.py, manual configuration is + ;; the preferred way of "searching" for inputs. + ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter. + (lambda* (#:key inputs #:allow-other-keys) + (let ((jpeg (assoc-ref inputs "libjpeg")) + (zlib (assoc-ref inputs "zlib")) + (tiff (assoc-ref inputs "libtiff")) + (freetype (assoc-ref inputs "freetype"))) + (substitute* "setup.py" + (("JPEG_ROOT = None") + (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")")) + (("ZLIB_ROOT = None") + (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")")) + (("TIFF_ROOT = None") + (string-append "TIFF_ROOT = libinclude(\"" tiff "\")")) + (("FREETYPE_ROOT = None") + (string-append "FREETYPE_ROOT = libinclude(\"" + freetype "\")"))))) + %standard-phases))) + (home-page "http://www.pythonware.com/products/pil/") + (synopsis "Python Imaging Library") + (description "The Python Imaging Library (PIL) adds image processing +capabilities to the Python interpreter.") + (license (license:x11-style + "file://README" + "See 'README' in the distribution.")))) + +(define-public python2-piddle-gn + (package + (name "python2-piddle") + (version "1.0.15-gn") + (source (origin + (method url-fetch) + (uri (string-append + "http://files.genenetwork.org/software/contrib/piddle-" +version ".tgz")) + (sha256 + (base32 + "05gjnn31v7p0kh58qixrpcizcxqf3b7zv4a5kk8nsmqwgxh0c6gq")))) + + (build-system python-build-system) + (native-inputs + `(("python2-setuptools" ,python2-setuptools))) + (arguments + `( + #:python ,python-2 + #:tests? #f ; no 'setup.py test' really! + )) + (home-page #f) (synopsis "Canvas drawing library for python2 (old!)") (description #f) (license #f))) |