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-rw-r--r--gn/packages/genenetwork.scm34
-rw-r--r--gn/packages/python.scm99
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)))