[galaxy-dev] Emailing to all our Galaxy users

2012-08-06 Thread Joachim Jacob
Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

Re: [galaxy-dev] Emailing to all our Galaxy users

2012-08-06 Thread Peter Cock
On Mon, Aug 6, 2012 at 9:14 AM, Joachim Jacob joachim.ja...@vib.be wrote: Dear devs, How can I extract a list of the email addresses of all users of our Galaxy? Cheers, Joachim Do you mean the registered accounts on your local Galaxy instance? This lives in the database of course, but is

Re: [galaxy-dev] Emailing to all our Galaxy users

2012-08-06 Thread Hans-Rudolf Hotz
Hi Joachim Go to Admin Menu - Security - Manage users. This will give you a list of all users. Alternatively, use the reports tool: Users - Date of last login and select 0 days Hope this helps, Regards, Hans On 08/06/2012 10:14 AM, Joachim Jacob wrote: Dear devs, How can I extract a

Re: [galaxy-dev] Emailing to all our Galaxy users

2012-08-06 Thread Joachim Jacob
Dear Peter and Hans-Rudolf, Everyday I learn something new about Galaxy :-) Thanks for pointing out the run_reports.sh service! This feels like what I need. Somehow I had never heard of it... Cheers, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34

[galaxy-dev] queue question

2012-08-06 Thread Zwemer, Lillian
Hi There, I'm not sure if this is the correct address to email to, so apologies in advance if I am in error. I am using the Galaxy Main (publicly available) site. I am wondering if there is a way to tell where my job is in the queue - in other words, how long it will be until my job begins to

[galaxy-dev] Different User with Torque

2012-08-06 Thread Wood, James, D
I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a

Re: [galaxy-dev] Different User with Torque

2012-08-06 Thread Oleksandr Moskalenko
On Aug 6, 2012, at 1:01 PM, Wood, James, D james.wo...@topper.wku.edu wrote: I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the

[galaxy-dev] Galaxy output not showing on tool success, indicating job failure.

2012-08-06 Thread John Patterson
Hello. I am an undergraduate working on a tool very similar to Tophat. My question is probably very basic, but I am having issues displaying the output. I am assuming is giving me the failed run boxes, even though my tool completes execution and generates its files. Note that I am not working

[galaxy-dev] How to configure samtools in galaxy on cluster

2012-08-06 Thread michael xu
Recently, I am trying to configure our galaxy on our cluster with PBS submission. I run galaxy locally very well on the head node, but I met one issue when I tried to configure galaxy on our cluster. In universe_wsgi.ini file, I added the following entries, start_job_runners = pbs

Re: [galaxy-dev] Different User with Torque

2012-08-06 Thread Oleksandr Moskalenko
It looks like the Torque provided libdrmaa.so does not support DRMAA native options. I built a 3rd party library (http://apps.man.poznan.pl/trac/pbs-drmaa/wiki) and was able to successfully run text galaxy jobs under a real user id with a correct resource request specified through the dynamic

[galaxy-dev] Error on database_connection statement in universe_wsgi.ini file

2012-08-06 Thread Kenneth Auerbach
Hello, Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the database_connection statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks! -Wolf. Modification to