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;; 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)
(targets '("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
<VirtualHost *:" (number->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
<Directory " ucsc-genome-browser "/html>
Options +Includes
#Options +Includes +FollowSymLinks +Indexes
AllowOverride None
<IfModule mod_authz_host.c>
Require all granted
SSILegacyExprParser on
</IfModule>
</Directory>
ScriptAlias /cgi-bin " ucsc-genome-browser "/cgi-bin
<Directory " 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
</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
Order allow,deny
Allow from all
</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=/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
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