galaxy config from 17.05 to 18.05

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galaxy config from 17.05 to 18.05

fernandez Edgar

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 = [hidden email]

---

> #error_email_to = None

493c483

< email_from = Galaxy ESI Project <[hidden email]>

---

> #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 = [hidden email]

---

> #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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Re: galaxy config from 17.05 to 18.05

fernandez Edgar

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: [hidden email]

542a565

>   email_from: Galaxy ESI Project <[hidden email]>

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: [hidden email]

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: '[hidden email]' <[hidden email]>
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 = [hidden email]

---

> #error_email_to = None

493c483

< email_from = Galaxy ESI Project <[hidden email]>

---

> #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 = [hidden email]

---

> #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

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/