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authorpjotrp2016-02-13 16:08:29 +0100
committerpjotrp2016-02-13 16:08:29 +0100
commit308bc003b2b7ba0669ef1b3e55063838faa9383c (patch)
tree54cbdd7ce7a58c414d7a9a8131e2c994f652540d
parente1e1e6c0c9b582bbdec5fcd7642868d0ca08301c (diff)
downloadguix-bioinformatics-308bc003b2b7ba0669ef1b3e55063838faa9383c.tar.gz
Settled on the GN version of htmlgen
-rw-r--r--gn/packages/bioinformatics.scm2
-rw-r--r--gn/packages/python.scm81
2 files changed, 16 insertions, 67 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 69a98c6..35ff166 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -233,7 +233,7 @@ confidence region for the location of a putative QTL.")
("mysql" ,mysql)
("nginx" ,nginx)
("python2-flask" ,python2-flask)
- ("python2-htmlgen" ,python2-htmlgen)
+ ("python2-htmlgen-gn" ,python2-htmlgen-gn)
("python2-jinja2" ,python2-jinja2)
("python2-sqlalchemy" ,python2-sqlalchemy)
("python2-setuptools" ,python2-setuptools)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index a5d71f6..09251d7 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -273,79 +273,24 @@ powerful language for representing information.")
(define-public python2-mysqlclient
(package-with-python2 python-mysqlclient))
-(define-public python2-htmlgen-old
-(package
- (name "python2-htmlgen-old")
- (version "2.2.2")
- (source (origin
- (method url-fetch)
- (uri (string-append
- "http://ftp.nl.debian.org/debian/pool/main/h/htmlgen/htmlgen_"
-version ".orig.tar.gz"))
- (sha256
- (base32
- "186kb434q6z84g31ysvzi4kcfcvl3pmm57k4jlng4ccgls94x6wb"))
- (patches (list
- (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
- (search-patch "python2-htmlgen-Fix-test-for-random.patch")
- ))))
- (build-system gnu-build-system)
- (outputs
- '("out"))
- (native-inputs `(("tar" ,tar)
- ("gzip" ,gzip)))
- (inputs
- `(("make" ,gnu-make)))
- (propagated-inputs
- `(("python2" ,python-2)))
- (arguments
- `(#:modules ((guix build utils))
- #:builder
- (let* ((source (assoc-ref %build-inputs "source"))
- (tar (assoc-ref %build-inputs "tar"))
- (gzip (assoc-ref %build-inputs "gzip"))
- (output (assoc-ref %outputs "out"))
- (srcdir (string-append output "/src"))
- (lib (string-append (assoc-ref %outputs "out") "/lib/htmlgen"))
- (python (string-append (assoc-ref %build-inputs "python2") "/bin/")))
- (begin
- (use-modules (guix build utils))
- (setenv "PATH" (string-append gzip "/bin")) ;; for tar
- ;; (setenv "PATH" (string-append python "/bin"))
- (system* (string-append tar "/bin/tar") "xzf"
- source)
- (chdir ,(string-append name "-" version))
- (mkdir-p srcdir)
- (lambda _
- (system* "python" "-m" "compileall" "."))
- (lambda _
- (system* "make" "test"))
- (mkdir-p lib)
- ; (copy-file "." lib)
- (copy-file "HTMLgen.pyc" lib)
- ))))
- (home-page
- "https://packages.debian.org/unstable/python/python-htmlgen")
- (synopsis "Python2 HTMLgen (somewhat defunkt project)")
- (description #f)
- (license #f)))
-(define-public python2-htmlgen
+(define-public python2-htmlgen-gn
(package
- (name "python2-htmlgen")
+ (name "python2-htmlgen-gn")
(version "2.2.2")
(source (origin
(method url-fetch)
+ ;; http://files.genenetwork.org/software/contrib/htmlgen-2.2.2-gn.tar.gz
(uri (string-append
- "http://ftp.nl.debian.org/debian/pool/main/h/htmlgen/htmlgen_"
-version ".orig.tar.gz"))
+ "http://files.genenetwork.org/software/contrib/htmlgen-"
+version "-gn.tar.gz"))
(sha256
(base32
- "186kb434q6z84g31ysvzi4kcfcvl3pmm57k4jlng4ccgls94x6wb"))
- (patches (list
- (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
- (search-patch "python2-htmlgen-Fix-test-for-random.patch")
- ))))
+ "1lwsk56rymhrma46cbyh3g64ksmq1vsih3qkrc2vh0lpba825y7r"))
+ ;;(patches (list
+ ;; (search-patch "python2-htmlgen-Applied-Deb-patch.patch")
+ ;; (search-patch "python2-htmlgen-Fix-test-for-random.patch")
+ ))
(build-system python-build-system)
(outputs '("out"))
(native-inputs
@@ -370,13 +315,17 @@ version ".orig.tar.gz"))
;; (copy-file "HTMLgen.pyc" "HTMLgen2.pyc")
(install-file "HTMLgen.pyc" lib)
(install-file "HTMLgen2.pyc" lib)
+ (install-file "imgsize.pyc" lib)
+ (install-file "ImageH.pyc" lib)
+ (install-file "ImagePaletteH.pyc" lib)
(install-file "__init__.pyc" lib)
))) ; install
) ; phases
#:tests? #f))
(home-page
"https://packages.debian.org/unstable/python/python-htmlgen")
- (synopsis "Python2 HTMLgen (somewhat defunkt project)")
+ (synopsis "Genenetwork version of Python2 HTMLgen (defunkt
+project)")
(description #f)
(license #f)))