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authorEfraim Flashner2020-07-26 15:21:30 +0300
committerEfraim Flashner2020-07-26 15:21:30 +0300
commit398759fae8ccf4354e751cc3405e0a486bf39439 (patch)
tree9723dcbc8c55270b48883f22507156b3ba2ef7cd /gn/services/genenetwork.scm
parent051d2fc1f66c84c1ea0da0e49fa6712eb07414fa (diff)
downloadguix-bioinformatics-398759fae8ccf4354e751cc3405e0a486bf39439.tar.gz
A running genenetwork
Diffstat (limited to 'gn/services/genenetwork.scm')
-rw-r--r--gn/services/genenetwork.scm35
1 files changed, 22 insertions, 13 deletions
diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index bf09270..8f5bfc4 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -9,12 +9,6 @@
(use-service-modules web)
(use-package-modules python)
-(define %python-path
- "/lib/python2.4/site-packages")
-
-(define %mod-python-path
- (file-append httpd22-mod-python-24 %python-path))
-
(define %default-httpd22-modules
(map (match-lambda
((name file)
@@ -85,7 +79,10 @@
python24-qtlreaper
python24-htmlgen-GN1
python24-json-GN1
+ python24-mysqlclient ; MySQLdb
+ python24-numarray
python24-piddle
+ python24-pp-GN1
python24-pyx-GN1
python24-pyxlwriter
python24-svg-GN1
@@ -97,13 +94,13 @@
(config
(httpd-config-file
(server-name "www.genenetwork.org")
- ;; Defaults to httpd, largely irrelevant.
+ ;; Defaults to httpd, should be same as 'package' above.
(server-root httpd22-mod-python-24)
(user "nobody")
(group "root")
+ ;; Only while debugging
(pid-file "/tmp/httpd-genenetwork1")
(error-log "/tmp/httpd-genenetwork1-error-log")
- (document-root (file-append genenetwork1 "/web"))
(listen '("8042"))
(modules (cons*
(httpd-module
@@ -111,20 +108,32 @@
(file "modules/mod_python.so"))
%default-httpd22-modules))
(extra-config (list "\
-TypesConfig etc/httpd/mime.types
+TypesConfig " httpd22-mod-python-24 "/etc/httpd/mime.types
DefaultType application/octet-stream
-#DocumentRoot MUST NOT be in the PythonPath
-PythonPath \"['/run/current-system/profile/lib/python2.4', '" httpd22-mod-python-24 "/lib/python2.4/site-packages']\"
+# DocumentRoot MUST NOT be in the PythonPath. Because genenetwork1 must be in PythonPath we leave the document-root keyword above unset.
+PythonPath \"['/run/current-system/profile/lib/python2.4', '/run/current-system/profile/lib/python2.4/site-packages', '" httpd22-mod-python-24 "/lib/python2.4/site-packages', '" genenetwork1 "/web/webqtl']\"
+# same as 'listen' above
+NameVirtualHost *:8042
+<VirtualHost *:8042>
+ DocumentRoot "genenetwork1 "/web
+</VirtualHost>
<Directory " genenetwork1 "/web/webqtl>
+ PythonOption session FileSession
+ #what is the difference between these two?
#AddHandler mod_python .py
SetHandler python-program
+ #publisher has more debug information
+ PythonHandler " genenetwork1 "/web/webqtl/main.py
#PythonHandler mod_python.publisher
- PythonHandler mod_python.cgihandler
- #PythonAutoReload Off
+ #PythonHandler mod_python.cgihandler
# only while debugging:
PythonDebug On
</Directory>
+# only while debugging:
<Location /mpinfo>
SetHandler python-program
PythonHandler mod_python.testhandler
</Location>")))))))))
+
+;; guix system container -L /path/to/guix-past/modules/ -L /path/to/guix-bioinformatics/ /path/to/guix-bioinformatics/gn/services/genenetwork.scm --network
+;; xdg-open http://localhost:8042