;; See dockerfile for some clarification about choices: ;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile ;; http://genome.ucsc.edu/goldenPath/help/mirrorManual.html (define-module (gn services genome-browser)) (use-modules (gnu) (guix build utils) (guix packages) (gn packages bioinformatics)) (use-service-modules databases networking web) (use-package-modules bash databases ghostscript wget) (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=penguin2\n" "db.user=webqtlout\n" "db.password=webqtlout\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. "slow-db.host=genome-mysql.soe.ucsc.edu\n" "slow-db.user=genomep\n" "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=penguin2\n" "central.user=webqtlout\n" "central.password=webqtlout\n" "central.domain=\n" "backupcentral.db=hgcentral\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=" 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 (define %startup-script (mixed-text-file "create_databases.sh" wget "/bin/wget http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql\n" 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/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. 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 4322) (operating-system (host-name "genome-browser") (timezone "Etc/UTC") (locale "en_US.utf8") (bootloader (bootloader-configuration (bootloader grub-bootloader) (target "does-not-matter"))) (file-systems %base-file-systems) ;; No firmware for VMs (firmware '()) (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 (service special-files-service-type `(;("/root/create_hgcentral" ,%startup-script) ("/var/lib/genome/hg.conf" ,%hg.conf))) (service inetd-service-type (inetd-configuration (entries (list (inetd-entry (node "127.0.0.1") (name "blat") ; yes, it's named blat (socket-type 'stream) (protocol "tcp") ; probably? (wait? #f) (user "httpd:httpd") ; or dedicated user. Needs write access. (program (file-append ucsc-genome-browser "/bin/gfServer")) (arguments '("gfServer" "dynserver" "/gbdb"))))))) (syslog-service) ; needed by inetd (service httpd-service-type (httpd-configuration (config (httpd-config-file (document-root (file-append ucsc-genome-browser "/html")) (server-name "Genome_Browser") (listen (list (number->string ucsc-genome-browser-port))) (modules (cons* (httpd-module (name "cgid_module") (file "modules/mod_cgid.so")) (httpd-module (name "include_module") (file "modules/mod_include.so")) %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 string ucsc-genome-browser-port) "> 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 /htdocs " ucsc-genome-browser "/html Alias /var/www/html/trash /var/cache/genome Alias /var/cache/genome /var/cache/genome Options +Includes #Options +Includes +FollowSymLinks +Indexes AllowOverride None Require all granted SSILegacyExprParser on ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin AllowOverride None Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch #Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch +Includes +FollowSymlinks Order allow,deny #SetHandler cgi-script Require all granted Allow from all Options MultiViews AllowOverride None Order allow,deny Allow from all # Upstream default location, possibly expected by software Options MultiViews AllowOverride None Order allow,deny Allow from all "))))))))) ;; 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:4322