diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 25 |
1 files changed, 13 insertions, 12 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a8ebe68..58110a7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages elf) #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) + #:use-module (gnu packages ghostscript) #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) @@ -1609,10 +1610,12 @@ multiple sequence alignment.") (substitute* (cons* "inc/cgi_build_rules.mk" (find-files "." "makefile")) (("CGI_BIN\\}-\\$\\{USER") "CGI_BIN_USER")) + ;; Force linking with freetype. (substitute* "inc/common.mk" (("libpng-config --ldflags") "pkg-config --libs libpng freetype2") (("libpng-config --I_opts") "pkg-config --cflags-only-I libpng freetype2")) + ;; Force the trash location. (substitute* (cons* "utils/qa/showTracks" @@ -1620,12 +1623,11 @@ multiple sequence alignment.") "hg/js/hgTracks.js" (find-files "." "\\.c$")) ;; This line is specifically needed as-is. - (("\\.\\./trash") "/var/www/html/trash")) + (("\\.\\./trash") "/var/cache/genome")) #t))) ;; Install happens during the 'build phase. ;; Install the website files too - ;; rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/html/ (replace 'install (lambda _ (invoke "make" "doc-install") @@ -1639,15 +1641,13 @@ multiple sequence alignment.") "include /var/lib/genome/hg.conf\n"))) #t))) (add-after 'install 'create-symlink - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; Some trash locations are hardcoded as "../trash" - ;(symlink "/var/www/html/trash" - ; (string-append out "/trash")) - (symlink "../html" - (string-append out "/htdocs")) - #t))) - ))) + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "htdocs") + ;; Fallback location for fonts. + (symlink (string-append (assoc-ref inputs "gs-fonts") + "/share/fonts/type1/ghostscript") + "htdocs/urw-fonts") + #t))))) (inputs `(("freetype" ,freetype) ("libpng" ,libpng) @@ -1658,7 +1658,8 @@ multiple sequence alignment.") ("python2" ,python-2) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config) + `(("gs-fonts" ,gs-fonts) + ("pkg-config" ,pkg-config) ("python" ,python) ("rsync" ,rsync) ; For installing js files from the source checkout ("tcl" ,tcl) |