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

> 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>

</handlers>

<destination id="torque" runner="drmaa"><param id="native_specification">-l nodes=1:ppn=8</param></destination>

</destinations>

<tools>

</tools>

</job_conf>

Finally,

cat /etc/httpd/vhosts.d/galaxy_prod.conf

User galaxy

Group users

Listen 8081

NameVirtualHost *: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

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

ExpiresActive On

ExpiresDefault "access plus 24 hours"

</Location>

# serve visualization and interactive environment plugin static content

AllowOverride None

Require all granted

</Directory>

RewriteRule ^/galaxy-prod/plugins/(.+)/(.+)/static/(.*)$ /home/galaxy/galaxy-prod/config/plugins/$1/$2/static/$3 [L]

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.ca

---

> #error_email_to = None

493c483

< email_from = Galaxy ESI Project <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

---

> #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