diff options
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/genome-browser.scm | 81 |
1 files changed, 58 insertions, 23 deletions
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm index 1a5b678..9da7535 100644 --- a/gn/services/genome-browser.scm +++ b/gn/services/genome-browser.scm @@ -4,6 +4,7 @@ (define-module (gn services genome-browser)) (use-modules (gnu) + (guix build utils) (guix packages) (gn packages bioinformatics)) (use-service-modules @@ -23,6 +24,7 @@ "db.user=readonly\n" "db.password=access\n" "db.trackDb=trackDb\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. @@ -46,8 +48,7 @@ ;"hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy" ;"hgc.ps2rasterPath=""/bin/ps2raster" "hgc.ghostscriptPath=" ghostscript "/bin/gs\n" ; needed? - "udc.cacheDir=/var/www/html/trash/udcCache\n" ; default is /tmp/udcCache - )) + "udc.cacheDir=/var/cache/genome/udcCache\n")) ; default is /tmp/udcCache (define %startup-script (mixed-text-file "create_databases.sh" @@ -55,18 +56,37 @@ bash-minimal "/bin/sh " (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh\n" mariadb "/bin/mysql -e \"create database hgcentral;\" mysql\n" mariadb "/bin/mysql hgcentral < hgcentral.sql\n" - coreutils-minimal "/bin/mkdir -p /var/www/html/trash\n" - coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n" - )) + coreutils-minimal "/bin/mkdir -p /var/cache/genome\n" + coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n")) + +;; This might be useful as a one-off shepherd job. +;(define %genome-activation-script +; #~(begin +; ;(unless (file-exists? "/var/lib/mysql/hgcentral") +; ; (invoke #$(file-append wget "/bin/wget") "http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql" "-O" "/var/lib/mysql/hgcentral.sql") +; ; ;(invoke "sh" #$(file-append (package-source ucsc-genome-browser) "/src/product/ex.MySQLUserPerms.sh")) +; ; (invoke #$(file-append mariadb "/bin/mysql") "-e" "\"create database hgcentral;\"" "mysql") +; ; (invoke #$(file-append mariadb "/bin/mysql") "hgcentral" "<" "/var/lib/mysql/hgcentral.sql")) +; (unless (file-exists? "/var/www/html/trash") +; (mkdir-p "/var/www/html/trash")) +; (unless (file-exists? "/var/cache/genome") +; (mkdir-p "/var/cache/genome")) +; (for-each (lambda (file) +; (chown file (passwd:uid "httpd") (passwd:gid "httpd"))) +; (append (find-files "/var/cache/genome" #:directories? #t) +; (find-files "/var/www/html/trash" #:directories? #t))) +; (for-each (lambda (file) +; (chown file (passwd:uid "mysql") (passwd:gid "mysql"))) +; (find-files "/var/lib/mysql" #:directories? #t)))) + +;(define %one-month-files +; (let ((%one-month (* 60 60 24 30))) +; (find-files "/var/cache/genome" (lambda (file stat) +; (> (stat:atime stat) %one-month))))) ;; TODO: -;; create 'daily clean' mcron scripts. -;; move /var/www/html/trash to /gbdb/trash? -;; Fix from main page: -;; hgVai -;; hgIntegrator -;; from 'more tools' -;; hgPhyloPlace +;; 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) @@ -81,10 +101,12 @@ (file-systems %base-file-systems) ;; No firmware for VMs (firmware '()) - (packages (cons* mariadb ; for create-db script + (packages (cons* mariadb ; for create-db script, interacting with database if necessary %base-packages)) (services - (list (service mysql-service-type) + (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) ("/var/lib/genome/hg.conf" ,%hg.conf))) @@ -121,19 +143,27 @@ %default-httpd-modules)) (extra-config (list "\ TypesConfig etc/httpd/mime.types +# More logs for more debugging. +LogFormat \"%h %l %u %t \\\"%r\\\" %>s %b\" common +CustomLog /var/log/httpd/combined_log common +#LogLevel debug # cgid.sock needs to be creatable, not in the store ScriptSock /var/run/cgid.sock +#XBitHack needs to not be inside the VirtualHost block. +XBitHack On # 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 # causes cgi scripts to fail to render + Alias /favicon.ico " ucsc-genome-browser "/html/faviconRR.ico Alias /htdocs " ucsc-genome-browser "/htdocs - #Alias /trash /var/www/html/trash # this is wrong - Alias /var/www/html/trash /var/www/html/trash + #Alias /htdocs " ucsc-genome-browser "/html + Alias /var/www/html/trash /var/cache/genome + Alias /var/cache/genome /var/cache/genome <Directory " ucsc-genome-browser "/html> - Options +Includes +FollowSymLinks +Indexes + Options +Includes + #Options +Includes +FollowSymLinks +Indexes AllowOverride None <IfModule mod_authz_host.c> Require all granted @@ -144,13 +174,21 @@ ScriptSock /var/run/cgid.sock ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin <Directory " ucsc-genome-browser "/cgi-bin> AllowOverride None - Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks + Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch + #Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks Order allow,deny #SetHandler cgi-script Require all granted Allow from all </Directory> + <Directory /var/cache/genome> + Options MultiViews + AllowOverride None + Order allow,deny + Allow from all + </Directory> + # Upstream default location, possibly expected by software <Directory /var/www/html/trash> Options MultiViews AllowOverride None @@ -159,8 +197,5 @@ ScriptSock /var/run/cgid.sock </Directory> </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=/path/to/gbdb=/gbdb -;; ALSO need to share in the external database? -;; Probably not, it falls back to http://hgdownload.soe.ucsc.edu/gbdb/ -;; Can skip the %startup-script dance if /var/lib/mysql is stored outside of the container, but might need /var/www/html/trash too then. +;; 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 |