- galaxy-dev - lists.galaxyproject.org

minimum AWS resources for TopHat?
by Andrew Norman 23 Jan '13

23 Jan '13

Hi all I'd like to use AWS EC2 cluster to run Galaxy TopHat to analyze the RNA seq data for my project. I'm trying to price out the resources that I'll need to do this, but I don't have any experience setting up clusters, virtual or real, so I'd like to get the insight of someone who has done this. I have studied the wiki page dedicated to this topic ( http://wiki.galaxyproject.org/CloudMan/AWS/CapacityPlanning) but I don't know how many worker nodes I'll need, and I will just be doing my personal analysis with this cluster (only one TopHat analysis at a time). Can anyone help me out with this? Thanks! Andy

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Job Update Time rollover at 24 hours
by Eric Enns 23 Jan '13

23 Jan '13

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different path for galaxy in cluster
by Hagai Cohen 23 Jan '13

23 Jan '13

Hi, I have a problem with my galaxy local installation working with a cluster. On the server my galaxy dir path is X, but on the cluster it is Y (same directory but different soft links). Is it possible to config the path of the galaxy installation (GALAXY_DIR) which will be send to the nodes? Thanks, Hagai

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Associate a user with a Galaxy user via e-mail like OpenID does
by Zinonas Antoniou 23 Jan '13

23 Jan '13

Hello, I have the connection using OAuth and I get the email of a user from other platform. Next, I want to associate this user with a user of Galaxy, like the OpenID does. Can anyone describe me explicitly the procedure should I do? What files should I change? Thank you in advance, Zinon

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Enhancing tool id="subtract_query1"
by Joachim Jacob 23 Jan '13

23 Jan '13

Hi all, One of our users had a problem, that the subtract datasets tool did not behave. She had just uploaded two datasets, one column each (actually in txt format), one with ~300000 lines, another with 106, and used the subtract tool. It did not work because of trailing white spaces (spaces, tabs and EOL) in the second file. Looking at the code, I had made a small adjustment then: adding a line: line = line.rstrip() (Line 32 in ~/galaxy-dist/tools/new_operations/subtract_query.py). Anyway, how to proceed that this fix is included in Galaxy main? I understand that these tools eventually will be migrated to the toolshed? Is it useful to do a pull request for this small enhancement? Or can somebody of the devteam add this patch? Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Upgrade Python to a newer version.
by Luobin Yang 23 Jan '13

23 Jan '13

Hi, Galaxy developers, My python version is 2.6.3 and I would like to upgrade it to 2.7.3. So is there anything that we need to on Galaxy after Python is upgraded to a new version? Thanks, Luobin

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Job handler keeps crashing
by Derrick Lin 22 Jan '13

22 Jan '13

Hi guys, We have updated our galaxy to 20 Dec 2012 release. Recently we found that some submitted jobs could not start (stay gray forever). We found that it was caused by the job manager sent jobs to a handler (handler0) whose python process crashed and died. >From the handler log we found the last messages right before the crash: galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 Stopping job 3032: galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 stopping job 3032 in drmaa runner We restarted the galaxy, handler0 is up for few seconds then died again with the same error messages except the job number moved to the next one. We observed that the jobs it was trying to stop are all previous jobs whose status is either "deleted" or "deleted_new". We have never seen this in the past, so wondering if there is bugs in the new release? Cheers, Derrick

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JAVAscript error after initiating tool
by Joachim Jacob 22 Jan '13

22 Jan '13

Hi all, For who is interested. Occasionally I get this strange Javascript error, just after clicking 'run' on a tool. ERROR updating hdas from api history contents:e47699a32b93ce7f The tool gets running, but the history panel is not updated. I click 'analyse data' to see the updated history. Cheers, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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ASCII and utf-8
by Anatoliy Pandorin 22 Jan '13

22 Jan '13

Hi, Thanks for your help! Have a problem: On some pages (in particular on the registration page, in .mako file) need to add comments (explanatory information in Cyrillic (need to use utf-8)). template`s files in ASCII. Maybe there is a traditional method of solving this problem with the encoding? Best regards, Anatoly

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deleted_new kills handlers
by Ido Tamir 22 Jan '13

22 Jan '13

Dear galaxy maintainers, we have the problem that killing jobs running on drmaa before they run leading to a deleted_new state, kills our handlers (sometimes?). The job gets sent to the handler, but the handler never acknowledges the jobs (local and drmaa) and all submitted jobs afterwards stay in submitted state. Normally submission works fine, running also. Is such a problem known to anybody else? in my universe_wsgi.ini: enable_job_recovery = False I don't know which other settings could affect this. Could it be an old drmaa library, maybe because the SGE was updated after galaxy installation? Other ideas? thank you very much, ido

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