diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/services/genome-browser.scm | 44 |
1 files changed, 25 insertions, 19 deletions
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm index 9da7535..a0947ec 100644 --- a/gn/services/genome-browser.scm +++ b/gn/services/genome-browser.scm @@ -20,11 +20,14 @@ (define %hg.conf (mixed-text-file "hg.conf" "browser.documentRoot=" ucsc-genome-browser "/html\n" - "db.host=localhost\n" - "db.user=readonly\n" - "db.password=access\n" + ;"db.host=localhost\n" + ;"db.user=readonly\n" + ;"db.password=access\n" + "db.host=penguin2\n" + "db.user=webqtlout\n" + "db.password=webqtlout\n" "db.trackDb=trackDb\n" - "db.port=13306\n" + ;"db.port=13306\n" "gbdbLoc1=/gbdb/\n" "gbdbLoc2=http://hgdownload.soe.ucsc.edu/gbdb/\n" ;# To disable on-the-fly loading of mysql data, comment out these lines. @@ -33,20 +36,23 @@ "slow-db.password=password\n" "defaultGenome=Mouse\n" "central.db=hgcentral\n" - "central.host=localhost\n" - "central.socket=/run/mysqld/mysqld.sock\n" ; default for mysql service - "central.user=readwrite\n" - "central.password=update\n" + ;"central.host=localhost\n" + ;"central.socket=/run/mysqld/mysqld.sock\n" ; default for mysql service + ;"central.user=readwrite\n" + ;"central.password=update\n" + "central.host=penguin2\n" + "central.user=webqtlout\n" + "central.password=webqtlout\n" "central.domain=\n" "backupcentral.db=hgcentral\n" - "backupcentral.host=localhost\n" - "backupcentral.user=readwrite\n" - "backupcentral.password=update\n" + "backupcentral.host=penguin2\n" + "backupcentral.user=webqtlout\n" + "backupcentral.password=webqtlout\n" "backupcentral.domain=\n" "freeType=on\n" "freeTypeDir=" gs-fonts "/share/fonts/type1/ghostscript\n" - ;"hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy" - ;"hgc.ps2rasterPath=""/bin/ps2raster" + ;"hgc.psxyPath=" gmt "/bin/psxy" + ;"hgc.ps2rasterPath=" gmt "/bin/ps2raster" "hgc.ghostscriptPath=" ghostscript "/bin/gs\n" ; needed? "udc.cacheDir=/var/cache/genome/udcCache\n")) ; default is /tmp/udcCache @@ -88,7 +94,7 @@ ;; create 'daily clean' mcron scripts. Only needed in /var/cache/genome grows too large. ;; use rsync to make sure mouse genome data is kept up-to-date. -(define ucsc-genome-browser-port 4321) +(define ucsc-genome-browser-port 4322) (operating-system (host-name "genome-browser") @@ -104,11 +110,11 @@ (packages (cons* mariadb ; for create-db script, interacting with database if necessary %base-packages)) (services - (list (service mysql-service-type - (mysql-configuration - (port 13306))) ; don't overlap with penguin2's mariadb + (list ;(service mysql-service-type + ; (mysql-configuration + ; (port 13306))) ; don't overlap with penguin2's mariadb (service special-files-service-type - `(("/root/create_hgcentral" ,%startup-script) + `(;("/root/create_hgcentral" ,%startup-script) ("/var/lib/genome/hg.conf" ,%hg.conf))) (service inetd-service-type (inetd-configuration @@ -198,4 +204,4 @@ XBitHack On </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 --share=/export/efraimf/UCSC_Genome/gbdb=/gbdb --share=/export/efraimf/UCSC_Genome/var-lib-mysql=/var/lib/mysql --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/cache/genome --share=/export/efraimf/UCSC_Genome/var-cache-genome=/var/www/html/trash -;; xdg-open http://localhost:4321 +;; xdg-open http://localhost:4322 |