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;; See dockerfile for some clarification about choices:
;; https://github.com/icebert/docker_ucsc_genome_browser/blob/master/Dockerfile
(define-module (gn services genome-browser))
(use-modules (gnu)
(gn packages bioinformatics)
)
(use-service-modules web)
(define %hg.conf
(mixed-text-file "hg.conf"
"browser.documentRoot=" ucsc-genome-browser "/html\n"
"db.host=gbdb\n"
"db.user=admin\n"
"db.password=admin\n"
"db.trackDb=trackDb\n"
"defaultGenome=Human\n"
"central.db=hgcentral\n"
"central.host=gbdb\n"
"central.user=admin\n"
"central.password=admin\n"
"central.domain=\n"
"backupcentral.db=hgcentral\n"
"backupcentral.host=gbdb\n"
"backupcentral.user=admin\n"
"backupcentral.password=admin\n"
"backupcentral.domain=\n"))
;; TODO: create 'daily clean' mcron scripts.
;; /var/www/html/trash needs to be created and owned by httpd:httpd
(define ucsc-genome-browser-port 4321)
(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* %base-packages))
(services
(list (service httpd-service-type
(httpd-configuration
(config
(httpd-config-file
(document-root (file-append ucsc-genome-browser "/html"))
(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
# cgid.sock needs to be creatable, not in the store
ScriptSock /var/run/cgid.sock
# 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
#Alias /cgi-bin/hg.conf " %hg.conf " # this doesn't seem to work
Alias /htdocs " ucsc-genome-browser "/htdocs
<Directory " ucsc-genome-browser "/html>
Options +Includes
SSILegacyExprParser on
</Directory>
ScriptAlias /cgi-bin/ " ucsc-genome-browser "/cgi-bin/
<Directory " ucsc-genome-browser "/cgi-bin>
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
#Order allow,deny
#Allow from all
SetHandler cgi-script
Require all granted
</Directory>
<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
;; ALSO need to share in the external database
;; xdg-open http://localhost:4321
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