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: edgar.fernandez@umontreal.ca
542a565
email_from: Galaxy ESI Project esi-galaxy-no-reply@umontreal.ca
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: rootbac@esi.umontreal.ca
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/$3 [L]
<Location "/"> XSendFile on XSendFilePath / </Location>
# Log levels LogLevel debug ErrorLog /var/log/httpd/galaxy-prod-error_log CustomLog /var/log/httpd/galaxy-prod-access_log common </VirtualHost>
Please let me know what you guys think...
Thank you,
Edgar Fernandez Administrateur Système (Linux) Technologies de l'Information Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210 * Bur. : 1-514-343-6111 poste 16568
From: Fernandez Edgar Sent: August 31, 2018 10:52 AM To: 'galaxy-dev@bx.psu.edu' galaxy-dev@bx.psu.edu Subject: galaxy config from 17.05 to 18.05
Hello gents,
I would greatly appreciate some help configuring my new installation of galaxy 18.05.
I found most of the configuration I needed but I'm missing the following configuration in green. Here is my galaxy 17.05: [galaxy@esilbac3a ~]$ 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 = edgar.fernandez@umontreal.camailto:edgar.fernandez@umontreal.ca ---
#error_email_to = None
493c483 < email_from = Galaxy ESI Project <rootbac@esi.umontreal.camailto:rootbac@esi.umontreal.ca> ---
#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 = rootbac@esi.umontreal.camailto:rootbac@esi.umontreal.ca ---
#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
galaxy-dev@lists.galaxyproject.org
-
Fernandez Edgar