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| author | Efraim Flashner | 2021-04-30 14:35:12 +0300 |
|---|---|---|
| committer | Efraim Flashner | 2021-04-30 14:49:05 +0300 |
| commit | 5e8b600b98dc058d3fc1d8bbda943ca9d8ac66f3 (patch) | |
| tree | 25f70f49229a2a1f46522fc2bf3a09701f2f3962 /gn/services | |
| parent | 7d8b95546ad7a90ccc9175e7a71a198f05f1b359 (diff) | |
| download | guix-bioinformatics-5e8b600b98dc058d3fc1d8bbda943ca9d8ac66f3.tar.gz | |
gn: genome-browser: update package, service
Diffstat (limited to 'gn/services')
| -rw-r--r-- | gn/services/genome-browser.scm | 35 |
1 files changed, 32 insertions, 3 deletions
diff --git a/gn/services/genome-browser.scm b/gn/services/genome-browser.scm index 7f7ffc0..1a5b678 100644 --- a/gn/services/genome-browser.scm +++ b/gn/services/genome-browser.scm @@ -8,6 +8,7 @@ (gn packages bioinformatics)) (use-service-modules databases + networking web) (use-package-modules bash @@ -42,7 +43,10 @@ "backupcentral.domain=\n" "freeType=on\n" "freeTypeDir=" gs-fonts "/share/fonts/type1/ghostscript\n" + ;"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 )) (define %startup-script @@ -55,8 +59,14 @@ coreutils-minimal "/bin/chown -R httpd:httpd /var/www\n" )) -;; TODO: create 'daily clean' mcron scripts. -;; /var/www/html/trash needs to be created and owned by httpd:httpd +;; TODO: +;; create 'daily clean' mcron scripts. +;; move /var/www/html/trash to /gbdb/trash? +;; Fix from main page: +;; hgVai +;; hgIntegrator +;; from 'more tools' +;; hgPhyloPlace (define ucsc-genome-browser-port 4321) @@ -78,6 +88,21 @@ (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 @@ -105,6 +130,8 @@ ScriptSock /var/run/cgid.sock Alias /bin " ucsc-genome-browser "/bin #Alias /cgi-bin " ucsc-genome-browser "/cgi-bin # causes cgi scripts to fail to render Alias /htdocs " ucsc-genome-browser "/htdocs + #Alias /trash /var/www/html/trash # this is wrong + Alias /var/www/html/trash /var/www/html/trash <Directory " ucsc-genome-browser "/html> Options +Includes +FollowSymLinks +Indexes AllowOverride None @@ -132,6 +159,8 @@ 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 ;--expose=/path/to/gbdb=/gbdb +;; 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. ;; xdg-open http://localhost:4321 |