6:40 p.m.
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(a)umontreal.ca
542a565
email_from: Galaxy ESI Project
<esi-galaxy-no-reply(a)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(a)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/$3 [L]
<Location "/">
XSendFile on
XSendFilePath /
</Location>
# Log levels
LogLevel debug
ErrorLog /var/log/httpd/galaxy-prod-error_log
CustomLog /var/log/httpd/galaxy-prod-access_log common
</VirtualHost>
Please let me know what you guys think...
Thank you,
Edgar Fernandez
Administrateur Système (Linux)
Technologies de l'Information
Université de Montréal
PAVILLON ROGER-GAUDRY, bureau X-210
* Bur. : 1-514-343-6111 poste 16568
From: Fernandez Edgar
Sent: August 31, 2018 10:52 AM
To: 'galaxy-dev(a)bx.psu.edu' <galaxy-dev(a)bx.psu.edu>
Subject: galaxy config from 17.05 to 18.05
Hello gents,
I would greatly appreciate some help configuring my new installation of galaxy 18.05.
I found most of the configuration I needed but I'm missing the following configuration
in green.
Here is my galaxy 17.05:
[galaxy@esilbac3a ~]$ 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.ca<mailto:edgar.fernandez@umontreal.ca>
---
#error_email_to = None
493c483
< email_from = Galaxy ESI Project
<rootbac@esi.umontreal.ca<mailto: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.ca<mailto: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
1358
days inactive
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days old
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Fernandez Edgar