Hey gents, I would really appreciate some help with this. If you can find some kind of error in my configuration.
I believe I have found all the configuration to run galaxy on port 7112 and have an apache proxy on 8081. Also I would like two handlers one for local and one for drama. I however still getting the following error in the apache logs: [Tue Sep 04 12:22:57 2018] [debug] mod_proxy_http.c(56): proxy: HTTP: canonicalising URL //localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(1544): [client 10.33.158.247] proxy: *: found reverse proxy worker for http://localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] mod_proxy.c(1026): Running scheme http handler (attempt 0) [Tue Sep 04 12:22:57 2018] [debug] mod_proxy_http.c(2018): proxy: HTTP: serving URL http://localhost:7112/ [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2102): proxy: HTTP: has acquired connection for (*) [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2158): proxy: connecting http://localhost:7112/ to localhost:7112 [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2289): proxy: connected / to localhost:7112 [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2540): proxy: HTTP: fam 2 socket created to connect to * [Tue Sep 04 12:22:57 2018] [debug] proxy_util.c(2672): proxy: HTTP: connection complete to 127.0.0.1:7112 (localhost) [Tue Sep 04 12:23:01 2018] [error] [client 10.33.158.247] (20014)Internal error: proxy: error reading status line from remote server localhost [Tue Sep 04 12:23:01 2018] [debug] mod_proxy_http.c(1499): [client 10.33.158.247] proxy: NOT Closing connection to client although reading from backend server localhost failed. [Tue Sep 04 12:23:01 2018] [error] [client 10.33.158.247] proxy: Error reading from remote server returned by /galaxy-prod/ [Tue Sep 04 12:23:01 2018] [debug] proxy_util.c(2120): proxy: HTTP: has released connection for (*) [Tue Sep 04 12:23:01 2018] [debug] mod_deflate.c(687): [client 10.33.158.247] Zlib: Compressed 497 to 333 : URL /galaxy-prod/ Hers is some of my config: diff galaxy.yml.sample galaxy.yml 19a20 > socket: 127.0.0.1:7112 24c25 < http: 127.0.0.1:8080 --- > #http: 127.0.0.1:8080 30c31 < buffer-size: 16384 --- > buffer-size: 32768 35c36 < processes: 1 --- > processes: 2 53c54 < master: false --- > master: true 68c69 < thunder-lock: false --- > thunder-lock: true 87a89,92 > mule: lib/galaxy/main.py > mule: lib/galaxy/main.py > farm: job-handlers:1,2 > 88a94 > server_name: main 93c99 < #filter-with: proxy-prefix --- > filter-with: proxy-prefix 100c106 < #cookie_path: null --- > cookie_path: /galaxy-prod 107a114 > database_connection: > mysql://galaxy:qaz1wsx2@localhost/galaxy_db_prod?unix_socket=/var/lib/mysql/mysql.sock 122a130 > database_engine_option_pool_recycle: 7200 168a177 > file_path: /home/galaxy/galaxy-prod/database/files 171a181 > new_file_path: /home/galaxy/galaxy-prod/database/tmp 177a188 > tool_config_file: > '/home/galaxy/galaxy-prod/config/tool_conf.xml,/home/galaxy/galaxy-prod/config/shed_tool_conf.xml' 192a204 > migrated_tools_config: > /home/galaxy/galaxy-prod/config/migrated_tools_conf.xml 199a212 > integrated_tool_panel_config: > /home/galaxy/galaxy-prod/config/integrated_tool_panel.xml 214a228 > tool_dependency_dir: /home/galaxy/galaxy-prod/database/dependencies 281a296 > tool_sheds_config_file: /home/galaxy/galaxy-prod/config/tool_sheds_conf.xml 342a358 > tool_data_table_config_path: > /home/galaxy/galaxy-prod/config/tool_data_table_conf.xml 351a368 > shed_tool_data_table_config: > /home/galaxy/galaxy-prod/config/shed_tool_data_table_conf.xml 441a459 > job_working_directory: /home/galaxy/galaxy-prod/database/jobs_directory 445a464 > cluster_files_directory: /home/galaxy/galaxy-prod/database/pbs 508a528 > smtp_server: smtp.umontreal.ca:25 522a543 > smtp_ssl: false 535a557 > error_email_to: [email protected] 542a565 > email_from: Galaxy ESI Project <[email protected]> 564a588 > user_activation_on: true 775a800 > apache_xsendfile: true 786a812 > upstream_gzip: false 989a1016 > use_interactive: false 1204a1232 > id_secret: 3s1G@l@xyPr0j3ct 1256a1285 > admin_users: [email protected] 1259a1289 > require_login: true 1263a1294 > show_welcome_with_login: true 1267a1299 > allow_user_creation: false 1270a1303 > allow_user_deletion: true 1273a1307 > allow_user_impersonation: true 1282a1317 > allow_user_dataset_purge: true 1288a1324 > new_user_dataset_access_role_default_private: true 1493a1530 > enable_quotas: true 1499a1537 > expose_dataset_path: true 1532a1571 > job_config_file: /home/galaxy/galaxy-prod/config/job_conf.xml 1622a1662 > cleanup_job: onsuccess Also, cat job_conf.xml <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/> </plugins> <handlers default="main.job-handlers.1"> <handler id="main.web.1" tags="handlers"><plugin id="local"/></handler> <handler id="main.job-handlers.1" tags="handlers"><plugin id="drmaa"/></handler> </handlers> <destinations default="torque"> <destination id="local" runner="local"></destination> <destination id="torque" runner="drmaa"><param id="native_specification">-l nodes=1:ppn=8</param></destination> </destinations> <tools> <tool id="upload1" handler="main" destination="local"/> </tools> </job_conf> Finally, cat /etc/httpd/vhosts.d/galaxy_prod.conf User galaxy Group users Listen 8081 NameVirtualHost *:8081 <VirtualHost *:8081> # don't decode encoded slashes in path info AllowEncodedSlashes NoDecode # enable compression on all relevant types AddOutputFilterByType DEFLATE text/html text/plain text/xml AddOutputFilterByType DEFLATE text/css AddOutputFilterByType DEFLATE application/x-javascript application/javascript application/ecmascript AddOutputFilterByType DEFLATE application/rss+xml AddOutputFilterByType DEFLATE application/xml AddOutputFilterByType DEFLATE application/json # allow access to static content <Directory "/home/galaxy/galaxy-prod/static"> AllowOverride None Require all granted </Directory> # allow up to 3 minutes for Galaxy to respond to slow requests before timing out ProxyTimeout 180 # uWSGI on a TCP socket ProxyPass /galaxy-prod/ uwsgi://127.0.0.1:7112/ # serve framework static content RewriteEngine On RewriteRule ^/galaxy-prod$ /home/galaxy/galaxy-prod/ [R] RewriteRule ^/galaxy-prod/static/style/(.*) /home/galaxy/galaxy-prod/static/style/blue/$1 [L] RewriteRule ^/galaxy-prod/static/(.*) /home/galaxy/galaxy-prod/static/$1 [L] RewriteRule ^/galaxy-prod/favicon.ico /home/galaxy/galaxy-prod/static/favicon.ico [L] RewriteRule ^/galaxy-prod/robots.txt /home/galaxy/galaxy-prod/static/robots.txt [L] RewriteRule ^/galaxy-prod(.*) http://localhost:7112$1 [P] # enable caching on static content <Location "/static"> ExpiresActive On ExpiresDefault "access plus 24 hours" </Location> # serve visualization and interactive environment plugin static content <Directory "/home/galaxy/galaxy-prod/config/plugins/(.+)/(.+)/static"> AllowOverride None Require all granted </Directory> RewriteRule ^/galaxy-prod/plugins/(.+)/(.+)/static/(.*)$ /home/galaxy/galaxy-prod/config/plugins/$1/$2/static/$3 [L] <Location "/"> XSendFile on XSendFilePath / </Location> # Log levels LogLevel debug ErrorLog /var/log/httpd/galaxy-prod-error_log CustomLog /var/log/httpd/galaxy-prod-access_log common </VirtualHost> Please let me know what you guys think... Thank you, Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568 From: Fernandez Edgar Sent: August 31, 2018 10:52 AM To: '[email protected]' <[email protected]> Subject: galaxy config from 17.05 to 18.05 Hello gents, I would greatly appreciate some help configuring my new installation of galaxy 18.05. I found most of the configuration I needed but I'm missing the following configuration in green. Here is my galaxy 17.05: [galaxy@esilbac3a ~]$ diff galaxy-17.05/config/galaxy.ini galaxy-17.05/config/galaxy.ini.sample 32c32 < port = 7112 --- > #port = 8080 37c37 < host = 0.0.0.0 --- > #host = 127.0.0.1 50,59d49 < # ---- HTTP PBS DRMAA HANDLER ----------------------------------------------- < < # Configuration of the pbs drmaa handler < < [server:handler0] < use = egg:Paste#http < port = 8088 < use_threadpool = True < threadpool_workers = 10 < 74c64 < prefix = /galaxy-prod --- > prefix = /galaxy 95c85 < filter-with = proxy-prefix --- > #filter-with = proxy-prefix 109c99 < database_connection = mysql://galaxy:qaz1wsx2@localhost/galaxy_db_prod2?unix_socket=/var/lib/mysql/mysql.sock --- > #database_connection = > sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE 119c109 < database_engine_option_pool_recycle = 7200 --- > #database_engine_option_pool_recycle = -1 152c142 < file_path = /home/galaxy/galaxy-prod/database/files --- > #file_path = database/files 155c145 < new_file_path = /home/galaxy/galaxy-prod/database/tmp --- > #new_file_path = database/tmp 161c151 < tool_config_file = /home/galaxy/galaxy-prod/config/tool_conf.xml,/home/galaxy/galaxy-prod/config/shed_tool_conf.xml --- > #tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml 197c187 < tool_dependency_dir = /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir --- > #tool_dependency_dir = database/dependencies 401c391 < job_working_directory = /home/galaxy/galaxy-prod/database/jobs_directory --- > #job_working_directory = database/jobs_directory 466c456 < smtp_server = smtp.umontreal.ca:25 --- > #smtp_server = None 475c465 < smtp_ssl = False --- > #smtp_ssl = False 486c476 < error_email_to = [email protected]<mailto:[email protected]> --- > #error_email_to = None 493c483 < email_from = Galaxy ESI Project <[email protected]<mailto:[email protected]>> --- > #email_from = None 679c669 < apache_xsendfile = True --- > #apache_xsendfile = False 693c683 < upstream_gzip = False --- > #upstream_gzip = False 848c838 < debug = False --- > #debug = False 861c851 < use_interactive = False --- > use_interactive = True 989c979 < id_secret = 3s1G@l@xyPr0j3ct --- > #id_secret = USING THE DEFAULT IS NOT SECURE! 1038c1028 < admin_users = [email protected]<mailto:[email protected]> --- > #admin_users = None 1041c1031 < require_login = True --- > #require_login = False 1049c1039 < allow_user_creation = False --- > #allow_user_creation = True 1052c1042 < allow_user_deletion = True --- > #allow_user_deletion = False 1055c1045 < allow_user_impersonation = True --- > #allow_user_impersonation = False 1060c1050 < allow_user_dataset_purge = True --- > #allow_user_dataset_purge = True 1066c1056 < new_user_dataset_access_role_default_private = True --- > #new_user_dataset_access_role_default_private = False 1200c1190 < enable_quotas = True --- > #enable_quotas = False 1234c1224 < job_config_file = /home/galaxy/galaxy-prod/config/job_conf.xml --- > #job_config_file = config/job_conf.xml 1292c1282 < retry_job_output_collection = 20 --- > #retry_job_output_collection = 0 1310c1300 < cleanup_job = onsuccess --- > #cleanup_job = always Please help me find what I am missing. Best regards, Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568
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