[galaxy-dev] galaxy config from 17.05 to 18.05

2018-08-31 Thread 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 = edgar.fernan...@umontreal.ca
---
> #error_email_to = None
493c483
< email_from = Galaxy ESI Project 
---
> #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 = root...@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

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[galaxy-dev] Setting up Galaxy Reports

2018-08-31 Thread Previti 
Dear Hans-Rudolf and list participants,

We would like to set up the galaxy reports tool on our version 17.09
instance and we succeeded partially after modifying the "reports.yml" to
point to our postgresql database.

The webpage is generated, with all the stats, but looks very basic and
the appropriate style-sheets are probably not found...

Any advise on how to set this up properly would be very welcome.

Best regards,

Christopher


On 08/17/2017 04:56 PM, Hans-Rudolf Hotz wrote:
> Hi Evan
>
> I assume you are talking about the 'reports' tool?
>
> Have a look here:
>
> https://galaxyproject.org/admin/usage-reports/
> https://docs.galaxyproject.org/en/latest/admin/reports.html
>
> Additional (system) information about each executed job can be logged
> by activating plugins in the "./config/job_metrics_conf.xml" file.
>
> https://galaxyproject.org/admin/config/job-metrics/
>
>
> Hope this helps
> Regards, Hans-Rudolf
>
>
>
> On 08/17/2017 04:25 PM, evan clark wrote:
>> I remember there previously being an additional tool that ran on a
>> different port from galaxy that allowed for monitoring of performance
>> and jobs running. Is this tool still packaged with galaxy and if so how
>> can it be activated.
>> ___
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-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de 
www.dkfz.de 

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