diff options
| author | Efraim Flashner | 2021-04-25 14:33:36 +0300 |
|---|---|---|
| committer | Efraim Flashner | 2021-04-25 14:58:42 +0300 |
| commit | 477b95399080a23b32c350b9ed8629898d033a9b (patch) | |
| tree | f815a70c2c1677f4baacc2d5495e96962ede8680 /gn/services/genome-browser.scm | |
| parent | 437219718f7bd189f0229570d4319d23aa3256aa (diff) | |
| download | guix-bioinformatics-477b95399080a23b32c350b9ed8629898d033a9b.tar.gz | |
gn: ucsc genome browser: functioning web service?
Diffstat (limited to 'gn/services/genome-browser.scm')
| -rw-r--r-- | gn/services/genome-browser.scm | 43 |
1 files changed, 27 insertions, 16 deletions
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 |