May 2012 - galaxy-dev - lists.galaxyproject.org

server error from history view while setting [debug=False]
by JIE CHEN 01 May '12

01 May '12

Dear all, When I check a new copy of galaxy source code(may 1st) and set [debug=False] in the universe_wsgi.ini, the history panel of the web UI can not be displayed properly. It says "server error". I did some searchings and find a thread http://gmod.827538.n3.nabble.com/Server-error-from-history-view-td1009053.h…. According to the thread, i think it is a problem long time ago. I don't know why it happens again. Anyone can tell me how to resolve the problem? I also tried the latest repository of galaxy-central. No luck either. Shall i just leave [debug=True] until the bug has been fixed. Thanks, Tyler

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Server error again from history view when setting [debug=False]
by JIE CHEN 01 May '12

01 May '12

Dear all, When I check a new copy of galaxy source code(may 1st) and set [debug=False] in the universe_wsgi.ini, the history panel of the web UI can not be displayed properly. It says "server error". I did some searchings and find a thread http://gmod.827538.n3.nabble.com/Server-error-from-history-view-td1009053.h…. According to the thread, i think it is a problem long time ago. I don't know why it happens again. Anyone can tell me how to resolve the problem? I also tried the latest repository of galaxy-central. No luck either. Shall i just leave [debug=True] until the bug has been fixed. Thanks, Tyler

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how to get "macs" not "macs14" for Galaxy
by Sergei Manakov 01 May '12

01 May '12

Hello, I am trying to set up MACS tool on local Galaxy. Galaxy comes with it's macs-wrapper.py and macs-wrapper.xml, but it wants to use "macs" not "macs14" executable. I tried to to editing macs-wrapper.py to make it use "macs14" instead, but some options are not the same between the two, and the tool crashes. I would appreciate if someone could give me an advice on where I can get "macs" executable for 64-bit Linux. thanks, Sergei -- Sergei (Siarhei Manakou) Manakov California Institute of Technology +1 626 395 3593

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Error message with terminated jobs
by Christophe Caron 01 May '12

01 May '12

Hi, We run Galaxy and Sun Grid Engine cluster environment (DRMAA API). When i start a job (e.g. : blast), the job runs on the cluster, and produces results output files. But in the history web interface, the job status is in error with this message : malloc: using debugging hooks /bin/sh: module: line 1: syntax error: unexpected end of file /bin/sh: error importing function definition for `module' malloc: using debugging hooks Any clue ? Thanks in advance -- Christophe Caron Station Biologique / Service Informatique et Bio-informatique Place Georges Teissier 29680 Roscoff Analysis and Bioinformatics for Marine Science http://abims.sb-roscoff.fr/ christophe.caron(a)sb-roscoff.fr tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77

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May 2012 Galaxy Update
by Dave Clements 01 May '12

01 May '12

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Remove libraries using Galaxy code or API
by liram_vardi＠agilent.com 01 May '12

01 May '12

Hello, I am using Galaxy API for some actions and I must say that this is indeed a really great feature with a great power. Anyway, I am trying to write a python script that one of its goals is to remove some data libraries, But until now, I was unable to find a way to remove data library or some of its datasets using the API or by direct call to Galaxy's code. I found a old post that claim that this feature is not yet implemented. My questions: 1) Is this has changed since? I mean, is there a way now to clean or remove completely a data library? 2) Is there a way to use Galaxy code to remove a library? Such as a function that can be used in my script to remove this library? Thanks in advance! Liram

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Job scheduling: FIFO, or fairer to multiple users?
by Peter Cock 01 May '12

01 May '12

Hello all, I'm curious if there is any way to manipulate the Galaxy job queuing in order to be 'fairer' to multiple simultaneous users. My impression is that Galaxy uses a simple FIFO queue itself, with for cluster jobs offloaded to the cluster queue immediately. In our case, I'm looking at large BLAST jobs (e.g. 20k queries against NR), which by their nature are easily subdivided between nodes (by dividing the query file up). We run these as one job per node (giving multiple cores for threading). That works nicely - the question I am currently pondering is tuning the split strategy, and multiple users. Specifically we get queue blocking if any one large BLAST jobs is divided into as many or more sub-jobs than we have cluster nodes in the BLAST queue. You can have one user's big BLAST job blocking multiple other user's small BLAST jobs even starting. I appreciate whether this is a problem will depend on the typical jobs run on each Galaxy instance, and the number and size of nodes in the local cluster - which makes a one-size-fits all strategy hard. I know that in order to be back-end agnostic, Galaxy takes limited advantage of different cluster backends - but perhaps the new 'run jobs as user' functionality might be helpful to allow the cluster to balance jobs between users? Is anyone doing that already? Another idea would be for Galaxy to manage its job queue on a user basis. Currently Galaxy submits all its jobs directly to the cluster, which can build up a backlog of pending jobs (whose scheduling is now out of Galaxy's control - probably simple FIFO depending on the cluster). Rather than giving the queued jobs to the cluster immediately, Galaxy could cache the jobs, and submit them gradually (monitor the cluster queue to see when it needs topping up). This would then enable Galaxy to interleave jobs from different users - any other queuing strategy. Too complicated? I think this is only a problem when the number of cluster nodes (in any given queue) is similar to or smaller than the number of parts a job might be broken up into. My guess is the public Galaxy doesn't do much job splitting (this code is quite new and not many of the wrappers exploit it), and has a large cluster. Is anyone else running into this kind of issues? Perhaps when Galaxy users are in competition with other cluster users? Thanks, Peter

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Is there a bowtie2 wrapper
by Oleksandr Moskalenko 30 Apr '12

30 Apr '12

I wonder if someone has a functional bowtie2 wrapper that they can share. Thanks, Alex

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