omero_config.txt000664 001750 001750 00000002057 12750051321 013701 0ustar00phmphm000000 000000 omero.data.dir=/OMERO omero.db.name=omero_database omero.db.pass=******** omero.db.user=db_omero omero.jvmcfg.percent.blitz=20 omero.jvmcfg.system_memory=32000 omero.mail.config=true omero.mail.host=smtp.college-de-france.fr omero.mail.password=******** omero.mail.port=25 omero.mail.username=philippe.mailly@college-de-france.fr omero.web.admins=[["Philippe Mailly", "philippe.mailly@college-de-france.fr"]] omero.web.application_server=wsgi-tcp omero.web.apps=["figure"] omero.web.debug=False omero.web.login_logo=/omero/static/webclient/image/logo_CIRB.jpg omero.web.prefix=/omero omero.web.public.enabled=False omero.web.session_cookie_age=86400 omero.web.session_expire_at_browser_close=True omero.web.static_url=/omero/static/ omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"target": "figure", "title": "Open Figure in new tab"}]] nginx_default.conf000664 001750 001750 00000002111 12750051750 014165 0ustar00phmphm000000 000000 server { listen 80; server_name localhost; #charset koi8-r; #access_log /var/log/nginx/log/host.access.log main; location / { root /usr/share/nginx/html; index index.html index.htm; } #error_page 404 /404.html; # redirect server error pages to the static page /50x.html # error_page 500 502 503 504 /50x.html; location = /50x.html { root /usr/share/nginx/html; } # proxy the PHP scripts to Apache listening on 127.0.0.1:80 # #location ~ \.php$ { # proxy_pass http://127.0.0.1; #} # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000 # #location ~ \.php$ { # root html; # fastcgi_pass 127.0.0.1:9000; # fastcgi_index index.php; # fastcgi_param SCRIPT_FILENAME /scripts$fastcgi_script_name; # include fastcgi_params; #} # deny access to .htaccess files, if Apache's document root # concurs with nginx's one # #location ~ /\.ht { # deny all; #} } omero_diags.txt000664 001750 001750 00000010174 12750051200 013516 0ustar00phmphm000000 000000 ================================================================================ OMERO Diagnostics 5.2.0-ice35-b12 ================================================================================ Commands: java -version 1.7.0 (/usr/java/latest/bin/java) Commands: python -V 2.7.5 (/opt/rh/python27/root/usr/bin/python -- 3 others) Commands: icegridnode --version 3.5.1 (/opt/Ice-3.5.1/bin/icegridnode -- 2 others) Commands: icegridadmin --version 3.5.1 (/opt/Ice-3.5.1/bin/icegridadmin -- 2 others) Commands: psql --version 9.4.8 (/usr/pgsql-9.4/bin/psql -- 2 others) Server: icegridnode running Server: Blitz-0 active (pid = 7492, enabled) Server: DropBox active (pid = 7512, enabled) Server: FileServer active (pid = 7555, enabled) Server: Indexer-0 active (pid = 7520, enabled) Server: MonitorServer active (pid = 7561, enabled) Server: OMERO.Glacier2 active (pid = 7521, enabled) Server: OMERO.IceStorm active (pid = 7534, enabled) Server: PixelData-0 active (pid = 7523, enabled) Server: Processor-0 active (pid = 7536, enabled) Server: Tables-0 active (pid = 7548, enabled) Server: TestDropBox inactive (enabled) Log dir: /opt/OMERO.server/var/log exists Log files: Blitz-0.log 357.0 MB errors=1152 warnings=2103 Log files: Blitz-0.log.1 524.0 MB errors=7091 warnings=7815 Log files: DropBox.log 8.0 KB errors=0 warnings=3 Log files: FileServer.log 1.0 KB Log files: Indexer-0.log 1.0 MB errors=3 warnings=6 Log files: MonitorServer.log 4.0 KB Log files: OMEROweb.lock 0.0 KB Log files: OMEROweb.log 1.0 MB errors=621 warnings=150 Log files: OMEROweb_brokenrequest.lock 0.0 KB Log files: OMEROweb_brokenrequest.log 0.0 KB Log files: PixelData-0.log 7.0 MB errors=1897 warnings=19 Log files: Processor-0.log 2.0 MB errors=715 warnings=3 Log files: Tables-0.log 6.0 KB errors=0 warnings=3 Log files: TestDropBox.log n/a Log files: master.err 169.0 KB errors=228 warnings=49 Log files: master.out 0.0 KB Log files: Total size 895.16 MB Environment:OMERO_HOME=(unset) Environment:OMERO_NODE=(unset) Environment:OMERO_MASTER=(unset) Environment:OMERO_USERDIR=(unset) Environment:OMERO_TMPDIR=/tmp Environment:PATH=/opt/Ice-3.5.1/bin:/opt/rh/python27/root/usr/bin:/usr/pgsql-9.4/bin/:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/opt/OMERO.server/bin:/opt/dell/srvadmin/sbin:/usr/java/latest/bin Environment:PYTHONPATH=/opt/Ice-3.5.1/python: Environment:ICE_HOME=(unset) Environment:LD_LIBRARY_PATH=/opt/Ice-3.5.1/lib64:/opt/Ice-3.5.1/lib:/opt/rh/python27/root/usr/lib64 Environment:DYLD_LIBRARY_PATH=(unset) OMERO SSL port:4064 OMERO TCP port:4063 OMERO data dir:'/OMERO' Exists? True Is writable? True OMERO temp dir:'/tmp' Exists? True Is writable? True (Size: 597664) JVM settings: Blitz-${index} -Xmx6400m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions JVM settings: Indexer-${index} -Xmx3200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions JVM settings: PixelData-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions JVM settings: Repository-${index} -Xmx3200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions OMERO.web status... [NOT STARTED] Django version: 1.8.6 ngnix_omero.conf000664 001750 001750 00000002631 12750051654 013674 0ustar00phmphm000000 000000 upstream omeroweb_omero { server 127.0.0.1:4080 fail_timeout=0; } server { listen 80; server_name omero.college-de-france.fr; rewrite ^ https://$server_name$request_uri? permanent; } server { listen 443 default ssl; server_name omero.college-de-france.fr; keepalive_timeout 70; ssl on; ssl_certificate /etc/nginx/omero.college-de-france.fr.crt; ssl_certificate_key /etc/nginx/omero.college-de-france.fr.key; ssl_protocols TLSv1 TLSv1.1 TLSv1.2; ssl_ciphers HIGH:!aNULL:!MD5; sendfile on; client_max_body_size 0; send_timeout 60s; # maintenance page serve from here location @maintenance_omero { root /opt/OMERO.server/etc/templates/error; try_files $uri /maintainance.html =502; } # weblitz django apps serve media from here location /omero/static { alias /opt/OMERO.server/lib/python/omeroweb/static; } location @proxy_to_app_omero { proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header Host $http_host; proxy_redirect off; proxy_set_header X-Forwarded-Proto $scheme; proxy_pass http://omeroweb_omero; } location /omero { error_page 502 @maintenance_omero; # checks for static file, if not found proxy to app try_files $uri @proxy_to_app_omero; } } ngnix.conf000664 001750 001750 00000001203 12750051564 012465 0ustar00phmphm000000 000000 user nginx; worker_processes 1; error_log /var/log/nginx/error.log warn; pid /var/run/nginx.pid; events { worker_connections 1024; } http { include /etc/nginx/mime.types; default_type application/octet-stream; log_format main '$remote_addr - $remote_user [$time_local] "$request" ' '$status $body_bytes_sent "$http_referer" ' '"$http_user_agent" "$http_x_forwarded_for"'; access_log /var/log/nginx/access.log main; sendfile on; #tcp_nopush on; keepalive_timeout 65; #gzip on; include /etc/nginx/conf.d/*.conf; }