diff options
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/bnw-container.scm | 32 | ||||
| -rw-r--r-- | gn/services/genome-browser.scm | 99 | ||||
| -rw-r--r-- | gn/services/gn1-httpd-config.scm | 18 |
3 files changed, 133 insertions, 16 deletions
diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm index 39da38d..b121bdb 100644 --- a/gn/services/bnw-container.scm +++ b/gn/services/bnw-container.scm @@ -2,9 +2,11 @@ (use-modules (gnu) (gn packages bnw) + (guix build utils) (guix records) (ice-9 match)) (use-service-modules networking web) +(use-package-modules base) (define-record-type* <bnw-configuration> bnw-configuration @@ -15,16 +17,22 @@ (deploy-directory bnw-deploy-directory ; string (default "/srv/http")) (port bnw-configuration-port ; list of strings - (default '("8880")))) + (default '("8881")))) (define bnw-activation (match-lambda - (($ <bnw-configuration> package deploy-directory port) + (($ <bnw-configuration> package _ port) #~(begin - (mkdir-p #$deploy-directory) - (copy-recursively #$package #$deploy-directory) - (invoke #$(file-append coreutils "/bin/chmod") "a+w" - (string-append #$deploy-directory "/sourcecodes/data")))))) + (let ((genenet "/var/lib/genenet/bnw") + (php-fpm-uid (passwd:uid (getpw "php-fpm"))) + (php-fpm-gid (passwd:gid (getpw "php-fpm")))) + (mkdir-p genenet) + (copy-recursively #$(file-append package "/var_lib_genenet_bnw") genenet) + (for-each (lambda (file-name) + (make-file-writable file-name) + (chown file-name php-fpm-uid php-fpm-gid)) + (find-files genenet + #:directories? #t))))))) (define bnw-nginx-config (match-lambda @@ -33,8 +41,8 @@ (nginx-server-configuration (server-name '("Bayesian Network")) (listen port) - ;(root package) - (root deploy-directory) + (root package) + ;(root deploy-directory) (locations (list (nginx-php-location) @@ -74,11 +82,13 @@ ;; No firmware for VMs. (firmware '()) ;; We don't need any packages inside the container. - (packages '()) + (packages (list coreutils)) (services (list (service dhcp-client-service-type) (service bnw-service-type ;; The following is for testing: - ;(bnw-configuration - ; (port '("8888"))) + (bnw-configuration + (port '("8888"))) )))) + +;; guix system container -L ~/workspace/guix-past/modules/ -L ~/workspace/guix-bioinformatics/ ~/workspace/guix-bioinformatics/gn/services/bnw-container.scm --network diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm new file mode 100644 index 0000000..58c8e4a --- /dev/null +++ b/gn/services/genome-browser.scm @@ -0,0 +1,99 @@ +;; 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 diff --git a/gn/services/gn1-httpd-config.scm b/gn/services/gn1-httpd-config.scm index a466097..6b2397d 100644 --- a/gn/services/gn1-httpd-config.scm +++ b/gn/services/gn1-httpd-config.scm @@ -62,6 +62,13 @@ ("alias_module" "modules/mod_alias.so") ("rewrite_module" "modules/mod_rewrite.so")))) +; Alternative setup +; (let* ((gn1-user "wrk") +; (gn1-source "/home/wrk/gn1-pjotr/gnshare/gn") +; (gn1-server "gn1-pjotr.genenetwork.org") +; (gn1-port "8043")) + + (define GN1-httpd-config (let* ((gn1-user "gn1") (gn1-source (string-append "/home/" gn1-user "/production/gnshare/gn")) @@ -117,12 +124,13 @@ NameVirtualHost *:" gn1-port " PythonHandler " gn1-source "/web/webqtl/main.py #PythonHandler mod_python.publisher #PythonHandler mod_python.cgihandler + PythonOption mod_python.session.session_type FileSession # only while debugging: - PythonOption mod_python.session.session_type MemorySession PythonDebug On </Directory> # only while debugging: -<Location /mpinfo> - SetHandler python-program - PythonHandler mod_python.testhandler -</Location>"))))) +# <Location /mpinfo> +# SetHandler python-program +# PythonHandler mod_python.testhandler +# </Location>" +))))) |