galaxy-dev August 2010

galaxy-dev@lists.galaxyproject.org

49 participants
62 discussions

swap issue
by Isabelle Phan 22 Mar '11

22 Mar '11

Hello, I am running galaxy, using a postgres backend. The galaxy server systematically gets killed whenever I try uploading a bam file. The samtools process is still running. This is the end of the log: 2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610 {'param_1': 8} sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371 {'param_1': 8} 2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection <connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var closed: 0> being returned to pool 10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1 (x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8" Killed I have the following options set in universe_wsgi.ini: database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal It seems to be running out of swap. I monitored memory usage with 'top' and galaxy died when available swap hit 0k free. I am not superuser on the machine where galaxy is running and I have no other server available. Is there something I could do to prevent galaxy from dying? Thanks, Isabelle -- Isabelle Phan, DPhil Seattle Biomedical Research Institute +1(206)256 7113

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user interface aspects don't show up right or look right in IE 7
by Leandro Hermida 01 Oct '10

01 Oct '10

Hello, I just had a look and see initially that certain aspects of the Galaxy UI don't show up or don't look right in IE 7, e.g. in the history pane the underlying link on the name of each data object to expand it isn't there. Is IE 7 supported? I dislike IE and don't use it otherwise but am forced to use it in my environment as it's part of there standard client image and it is almost impossible to get another browser like Firefox installed for every user that will use Galaxy. best, Leandro

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stupid logging question
by Michael Pheasant 07 Sep '10

07 Sep '10

Using the run.sh script, and the default 'log_level = DEBUG' universe_wsgi.ini file setting gives a huge amount of output. Changing the ini to either log_level = INFO, WARNING or ERROR and i get the same output, including the INFO messages every second. I assumed that WARNING or ERROR would not give the INFO messages; is there some way to not see these? Cheers m -- 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

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integrating genome view as a display application
by Marijn Vandevoorde 07 Sep '10

07 Sep '10

Hi all, I'm trying to integrate genomeview as a display application. The configuration of the display applications seems to be pretty straightforward, but genomeview needs multiple input files. I can of course write a cgi file that will take a bunch of get parameters and use these as input files for the java applet. so on the side of genomeview, there's not really a big problem. however, to integrate it with galaxy, i don't see how to send multiple datasets to genomeview. you can only add the "view with genomeview" link to one dataset (or to all, but all will be viewed seperately). so i came up with the idea of a new datatype, .gvl, the genomeview list. in it, basically, a list of links to the datasets, so galaxy can work with them. i could make a tool, gvl creator, to take several datasets as input and then create a really simple textfile containing one url per line, for each dataset. i think this is the way to go (if anyone has better suggestions, please tell!) but now come the real questions: most important: how do i get the public url of my datasets? all other tools use the filesystem path, can't really find an example. and secondly: any idea how i could maybe take a dynamic number of inputs? i suppose that's not possible. this is not that big a problem. i could combine multiple gvl creators and then a gvl merger or something, no biggie! all help really appreciated. and of course i'll be happy to share everything with whoever is interested afterwards :-) with kind regards, marijn -- Marijn Vandevoorde Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM marijn.vandevoorde(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== "If you type google into google, you can break the internet" --Jen Barber

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The job is finished..but not in the history
by amerite 02 Sep '10

02 Sep '10

hi, I'm writing some wrappers to connect galaxy with some scripts/programs. I can't understand why, for some, the job in the history never end. Here an example of the log output <output> 127.0.0.1 - - [20/Aug/2010:14:18:38 +0200] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" galaxy.jobs DEBUG 2010-08-20 14:18:41,524 job 81 dispatched galaxy.jobs.runners.local DEBUG 2010-08-20 14:18:41,694 executing: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20 127.0.0.1 - - [20/Aug/2010:14:18:42 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" 127.0.0.1 - - [20/Aug/2010:14:18:46 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... 127.0.0.1 - - [20/Aug/2010:14:19:18 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" galaxy.jobs.runners.local DEBUG 2010-08-20 14:19:20,831 execution finished: python /home/extuser/galaxy-dist/tools/myTools/wrapper_pileup.py --ir /home/extuser/raffo/chromosomes/hg19 --im /home/extuser/galaxy-dist/database/files/000/dataset_40.dat --out /home/extuser/galaxy-dist/database/files/000/dataset_87.dat --mm 20 127.0.0.1 - - [20/Aug/2010:14:19:22 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" 127.0.0.1 - - [20/Aug/2010:14:19:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.0.19) Gecko/2010072022 Iceweasel/3.0.6 (Debian-3.0.6-3)" ... ... ... and so on </output> If i check the "running" dataset clicking the eye i see the final result that I expect.... Then, checking in the table 'dataset' (in universe.sqlite) i obtain 87|running why the flag isn't changed to ok? any ideas? Tnx :) raf

2 2

Galaxy Genome Builds
by Anton Nekrutenko 31 Aug '10

31 Aug '10

Dear Galaxy user: Below are two important points about Galaxy genome builds that may affect your analysis results: 1. Canonical and Complete builds Many genomes provided by Galaxy originate from UCSC and are represented by a mix of canonical chromosomes (such as 1 through Y in mammals), mitochontrial genome (chrM), and unplaced fragments (chrUn) and/or haploblocks. Until last week we were using only canonical chromosomes and the mitochondrion to build indices required by NGS mappers (bwa, bowtie, bfast, lastz, and perm) and SAM Tools. However, for some analyses it is necessary to include regions that are not placed within the canonical chromosome set. Starting next week we will be providing two sets of NGS mapper indices: canonical (chr1 through chrY + chrM) and full (everything). A separate message will be sent out once this is enabled. 2. A recent un-announced change to hg19 The hg19 version of NGS and SAMTools indices contained only CANONICAL chromosomes (chr1 through Y + chrM) until August 20. On August 20 it was changed to the full version. As a result mapping jobs that were run after August 20, 2010 may return slightly different results. Anton Nekrutenko http://usegalaxy.org

1 0

galaxy user quotas?
by lentaing＠jimmy.harvard.edu 30 Aug '10

30 Aug '10

Hi, We would like to enforce a policy of setting user disk quotas to a maximum of 10GB/user on our galaxy instance. Is there a way to specify this in galaxy, e.g. in universe.ini? If it's not currently implemented, could you point me to some relevant locations in the galaxy source to help me get started? Thanks, Len Cistrome Development Team

2 1

links in param tags
by Belinda M. Giardine 27 Aug '10

27 Aug '10

Is it possible to include a link in the help attribute of the param tag set? Belinda

2 3

request_param_translation and request_param
by Erick Antezana 27 Aug '10

27 Aug '10

Hi, I've got some questions regarding some tags (e.g. request_param_translation and request_param). Their doc is fully described here: http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax 1. In the doc of 'request_param_translation', we find: "This tag set is contained within the <param> tag set - it contains a set of <request_param> tags." But it seems that it is not needed to include this tag set within the 'param' one (but directly child of the 'tool' tag)? 2. in the doc of 'request_param', there is a nice table with the attributes, values, etc. Is the value "URL_method" missing in that table as possible value? if so, what would be the difference between that definition and the one we set in the 'tool' tag? Is the list of possible values a comprehensive one? 3. The example of usage of 'request_param_tranlsation' has a typo: "requst_param_translation" instead of "request_param_translation". I guess that the suffixing "}" in the remote_name example (in the request_param table) should also be deleted? 4. is there any doc about the 'uihints' tag? (found in some examples such as ucsc_tablebrowser.xml). cheers, Erick

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Re: [galaxy-dev] [galaxy-bugs] AMI image
by Enis Afgan 26 Aug '10

26 Aug '10

Hi Loretta, Our AMI is hosted on Amazon as an EBS AMI so it is not possible to download it in its entirety. If you plan on using it on AWS, it is publicly available so you can use it or tweak it as desired. The EBS snapshot from which this AMI is derived is also publicly available as snap-d0a071b8. If you need to replicate the services/functionality included on this AMI outside AWS, we have a script that defines and automates the process of building the machine image using Python Fabric. The source code (with instructions on how to use it) is in the following repository: http://bitbucket.org/afgane/mi-deployment. Hope this helps, Enis > Hi, > > This is really a request... We have a cloud implementation and I was > wondering if you have or can make your AMI image (AMI: ami-ed03ed84) > available for download... > > Thanks... > > -Loretta > > *********************** > Loretta Auvil > lauvil(a)illinois.edu > 1205 W. Clark St, MC-257 > Urbana, IL 61801 > 217-265-8021 > > > > > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-bugs >

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galaxy-dev August 2010