diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 57 |
1 files changed, 33 insertions, 24 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index b836ff0..3785b0f 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages shells) #:use-module (gnu packages statistics) + #:use-module (gnu packages tcl) #:use-module (gnu packages time) #:use-module (gnu packages tls) #:use-module (gnu packages vim) @@ -1601,13 +1602,25 @@ multiple sequence alignment.") (setenv "DOCUMENTROOT_USER" (string-append out "/html")) (setenv "BINDIR" (string-append out "/bin")) - ;; Now let's fix some errors + ;; Now let's fix some errors: (mkdir-p (string-append out "/cgi-bin")) (substitute* "inc/cgi_build_rules.mk" (("rm -f.*") "")) (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" + "webBlat/webBlat.cfg" + "hg/js/hgTracks.js" + (find-files "." "\\.c$")) + ;; This line is specifically needed as-is. + (("\\.\\./trash") "/var/www/html/trash")) #t))) ;; Install happens during the 'build phase. @@ -1617,33 +1630,28 @@ multiple sequence alignment.") (lambda _ (invoke "make" "doc-install") #t)) - ;; TODO: Figure out how to make this configurable in the service. (add-after 'install 'create-hg-conf (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (with-output-to-file (string-append out "/cgi-bin/hg.conf") (lambda () (display - (string-append - "browser.documentRoot=" out "/html\n" - "db.host=gbdb\n" - "db.user=admin\n" - "db.password=admin\n" - "db.trackDb=trackDb\n" - "defaultGenome=Human\n" - "central.db=hgcentral\n" - "central.host=gbdb\n" - "central.user=admin\n" - "central.password=admin\n" - "central.domain=\n" - "backupcentral.db=hgcentral\n" - "backupcentral.host=gbdb\n" - "backupcentral.user=admin\n" - "backupcentral.password=admin\n" - "backupcentral.domain=\n")))) - #t)))))) + "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))) + ))) (inputs - `(("libpng" ,libpng) + `( + ("freetype" ,freetype) + ("libpng" ,libpng) ("mysql:dev" ,mariadb "dev") ("mysql:lib" ,mariadb "lib") ("openssl" ,openssl) @@ -1651,10 +1659,11 @@ multiple sequence alignment.") ("python2" ,python-2) ("zlib" ,zlib))) (native-inputs - `(;("python" ,python) + `(("pkg-config" ,pkg-config) + ("python" ,python) ("rsync" ,rsync) ; For installing js files from the source checkout - ;("tcl" ,tcl) - ;("tcsh" ,tcsh) + ("tcl" ,tcl) + ("tcsh" ,tcsh) ("util-linux:lib" ,util-linux "lib") ("which" ,(@ (gnu packages base) which)))) (home-page "https://www.genome.ucsc.edu/") |