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authorEfraim Flashner2021-05-10 08:59:29 -0500
committerEfraim Flashner2021-05-11 06:05:03 -0500
commitd0e75d0dfee30c3d1c6c98ef64a96366aa0c2ef9 (patch)
tree8b441476c4629bc56875692fc094dcc5b673d94e /gn/services
parent2d8a3551b41d27723471a9a5e5460706fe2d2d1f (diff)
downloadguix-bioinformatics-d0e75d0dfee30c3d1c6c98ef64a96366aa0c2ef9.tar.gz
gn: genome-browser: use database on penguin2
Diffstat (limited to 'gn/services')
-rw-r--r--gn/services/genome-browser.scm44
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