June 2010 - galaxy-dev - lists.galaxyproject.org

links missing on history items sometimes
by Michael Pheasant 02 Jun '10

02 Jun '10

Hi History items in the green boxes on the RHS of the galaxy screen usually have hyperlinks on the names. Cliking on the link expands or un-expands the text in the green box. Sometimes the links disappear on my instance, see the attached image (if its not stripped off by the mailing list). I havent been able to figure out why this happens or how to fix it. Is it controlled by an .ini file setting? Or something else? The session? Cheers Mike. -- Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 6, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org

3 3

display_application
by Davide Cittaro 02 Jun '10

02 Jun '10

Hi all, I've noticed that when I try to visualize a BAM file on UCSC (with display_application) the galaxy web process drains RAM and never releases it... I easly go in OutOfMemory error. Is it trying to load BAM (or any other custom file defined to be visualized in the same way) in RAM? Can anybody explain how display_application works and how to debug it? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

4 9

job recovery Q
by Michael Pheasant 01 Jun '10

01 Jun '10

In the ini file it says the option enable_job_recovery is not safe if you are running more than one galaxy server using the same database (see below). We have one job runner and multiple web servers. Is that 'safe'? Does the 'one Galaxy server' refer to one job runner or one web server? Cheers Mike. # Enable job recovery (if Galaxy is restarted while cluster jobs are running, # it can "recover" them when it starts). This is not safe to use if you are # running more than one Galaxy server using the same database. enable_job_recovery = True -- Michael Pheasant Software Engineer Queensland Facility for Advanced Bioinformatics Level 6, QBP University of Queensland, QLD 4072 T: +61 (0)7 3346 2070 F: +61 (0)7 3346 2101 www.qfab.org

2 1

Galaxy with non-SGE/non-Torque distributed jobs
by Andrey Tovchigrechko 01 Jun '10

01 Jun '10

We have decided to use a local Galaxy install as a front-end to our metagenomic binning tool MGTAXA ( http://andreyto.github.com/mgtaxa/ ) I need some guidance from the Galaxy developers for the best way to proceed: 1) The server will be on a DMZ, with no direct access to the internal network, where the computes will be running on a local SGE cluster. The best that our IT allowed is for some script on the internal cluster to monitor a directory on the web server, pull input/tasks from where when they appear, put the results back. My current idea is to have the Galaxy "local runner" to start "proxy jobs": each proxy job is a local process that does "put the input into watched dir; until results appear in the watched dir; sleep(30); loop; finish". In other words, Galaxy thinks that it is running jobs locally, but it fact those jobs are just waiting for the remote results to come back. Does that look like a sane solution? How will it scale on the Galaxy side? E.g. how many such simultaneous tasks can the local runner support? Any anticipated gotchas? Additionally, we will be also trying to run computes on our TeraGrid account. I was thinking that the solution above can be applied to that scenario also, except that now the proxy job would be polling qsub on TeraGrid through ssh, or call Globus API. Here one problem is that a job often has to wait in a TeraGrid queue for 24 hours or so. Will my proxy jobs on Galaxy time out/get killed by any chance? The alternatives are 1) write another runner (in addition to local, sge, torque) - how much work it will be? 2) write a fake SGE python interface and make Galaxy think it is using local SGE 2) What repo is best to clone, given the scope of our activity described above? We will likely need to mess a bit with the Galaxy internals, not just the tool definition. Should we clone galaxy-central or galaxy-dist? What workflow would you recommend for updating, submitting patches etc? I will be very grateful for answers to the above, and also to any alternative recommendations. Andrey

4 3

Sourcing Files from Datasets
by Dennis Gascoigne 01 Jun '10

01 Jun '10

We have put together a stack of our standard workflows in Galaxy and it is working well. Thanks. One feature that would be infiinitely useful - i.e. we would be using it now, would be the ability to source files from the data libraries. We know you can add an item to the history thourgh the data libraries interface, but having an input tool, and.or being able to select an input from the data libraries when using the workflow designer would be great. If this is ont something you are keen on, any pointers on the best way to implement this - i have some ideas but have no idea if they are the best way. Cheers Dennis

2 1

how to activate account to allow remote access?
by Edward Kirton 01 Jun '10

01 Jun '10

Hello, i recently switched to ldap authentication such that user accounts are automatically created. Everything works as it should on the intranet site, but when i try to log-on via our internet site, i get the following error: "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." Even if i create a password for the user, this message remains. How do i activate the account? Thanks, Ed

2 1

Integrating Galaxy into our Kerberos auth
by Peter van Heusden 01 Jun '10

01 Jun '10

Hi everyone I'm busy integrating Galaxy (installed locally on galaxy.sanbi.ac.za) with our Kerberos authentication. To do this, in the Apache virtualhost configuration, I install mdo_auth_kerb and specify: <Location /> AuthType Kerberos Krb5Keytab /etc/krb5.keytab KrbServiceName http KrbAuthRealms SANBI Require valid-user </Location> in my virtualhost config. Now, our Kerberos users show up as <user>@SANBI (SANBI is our realm). Their email addresses are of the form <user>@sanbi.ac.za. So this causes a problem with the default Galaxy config. The solution I've got is to throw away that @SANBI, then set remote_user_maildomain to sanbi.ac.za. And add this to the virtualhost config: RewriteEngine on <Proxy http://localhost:8080> Order deny,allow Allow from all </Proxy> RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} ^([^@]+)@ RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e Note the ^([^@]+)@ - this is different to the (.*) which is on the wiki, and has the effect that %1 in the RewriteRule only contains the <user> part. The remote_user_maildomain is then used to get <user>@sanbi.ac.za. So far this setup seems to work. BTW. why, in templates/webapps/galaxy/base_panels.mako does it only show the "Logged in as" if you are not using remote_user ? Since user_email is always generated somehow, surely it is safe to show it whether you're logged in via remote_user or not. And finally, I see that after the first few uploads, there aren't any new sets of slides being put up on the dev2010 page. I'm looking forward to seeing a full set of slides so I can show them to people at SANBI! Peter

2 1