diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 27 | ||||
| -rw-r--r-- | gn/services/genome-browser.scm | 43 |
2 files changed, 53 insertions, 17 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 76406db..b836ff0 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1616,7 +1616,32 @@ multiple sequence alignment.") (replace 'install (lambda _ (invoke "make" "doc-install") - #t))))) + #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)))))) (inputs `(("libpng" ,libpng) ("mysql:dev" ,mariadb "dev") diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm index 961569a..58c8e4a 100644 --- a/gn/services/genome-browser.scm +++ b/gn/services/genome-browser.scm @@ -1,3 +1,5 @@ +;; See dockerfile for some clarification about choices: +;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile (define-module (gn services genome-browser)) (use-modules (gnu) @@ -6,24 +8,26 @@ (use-service-modules web) (define %hg.conf - (plain-file "hg.conf" - (string-append "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"))) + (mixed-text-file "hg.conf" + "browser.documentRoot=" ucsc-genome-browser "/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")) ;; TODO: create 'daily clean' mcron scripts. +;; /var/www/html/trash needs to be created and owned by httpd:httpd (define ucsc-genome-browser-port 4321) @@ -57,11 +61,15 @@ %default-httpd-modules)) (extra-config (list "\ TypesConfig etc/httpd/mime.types +# cgid.sock needs to be creatable, not in the store +ScriptSock /var/run/cgid.sock # same as 'listen' above <VirtualHost *:" (number->string ucsc-genome-browser-port) "> XBitHack On DocumentRoot " ucsc-genome-browser "/html Alias /bin " ucsc-genome-browser "/bin + Alias /cgi-bin " ucsc-genome-browser "/cgi-bin + #Alias /cgi-bin/hg.conf " %hg.conf " # this doesn't seem to work Alias /htdocs " ucsc-genome-browser "/htdocs <Directory " ucsc-genome-browser "/html> Options +Includes @@ -72,6 +80,8 @@ TypesConfig etc/httpd/mime.types <Directory " ucsc-genome-browser "/cgi-bin> AllowOverride None Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch + #Order allow,deny + #Allow from all SetHandler cgi-script Require all granted </Directory> @@ -85,4 +95,5 @@ TypesConfig etc/httpd/mime.types </VirtualHost>"))))))))) ;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genome-browser.scm --network +;; ALSO need to share in the external database ;; xdg-open http://localhost:4321 |