Re: [galaxy-dev] Dynamic job runner configuration followup

2012-06-12 Thread Matloob Khushi
Dear John This sounds interesting, however, I've been struggling for quite a sometimes on limiting the number of options a user could see when it loads the tool wrapper. I have a separate database that records the results obtained from the execution of my developed tool along with the

Re: [galaxy-dev] Interested in speaking with other institutions deploying

2012-04-29 Thread Matloob Khushi
Hi Ann I am running an instance at The University of Sydney GMT+10 and would like to be part of any such online talk. Regards, Matloob ___ Please keep all replies on the list by using reply all in your mail client. To manage your

[galaxy-dev] Reading user id before the execution of the tool

2012-03-20 Thread Matloob Khushi
(**configuration ) But this generates following error. UnboundExecutionError: Parent instance History at 0x581cdd0 is not bound to a Session; lazy load operation of attribute 'active_datasets' cannot proceed Regards Matloob Khushi

[galaxy-dev] Writing a database interative tool

2012-02-06 Thread Matloob Khushi
Hi Galaxy Developers I aim to write a tool that will interact with Postgres database; here is what I wrote to test database connectivity. This script resides in /galaxy-dist/tools/test_tool/ and gets invoked from the front end. However script generate following error: No module named psycopg2.

[galaxy-dev] loading tool values from other databases

2012-02-02 Thread Matloob Khushi
Dear Galaxy Developers I wish to write set of tools for Galaxy Community; tools will use Postgresql/MySQL database (other than the default galaxy database). Tool's dropdown boxes will load values from the database on the fly. I had a look at tool configuration at Galaxy WiKi and I can't seems

Re: [galaxy-dev] Setting http_proxy for Python

2011-09-30 Thread Matloob Khushi
: Friday, 30 September 2011 5:39 AM To: Matloob Khushi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Setting http_proxy for Python Hi Matloob, It looks like urllib, which Galaxy uses to fetch eggs, can't use authenticated proxies. urllib2 would do it: http://stackoverflow.com