galaxy-dev November 2010

galaxy-dev@lists.galaxyproject.org

63 participants
98 discussions

why is my lastz process showing it is not finished?
by David Hoover 02 Dec '10

02 Dec '10

I've set up a local instance of Galaxy, and have submitted a lastz job on some fake data. It ran for about 3 minutes and then finished, as shown in the logfiles and by system tools like top and ps. However, the web page shows the spinning wheel and yellow box for 10 minutes until the box turned green and wheel stopped spinning. Why is there such a delay between when the job completes and when the web page shows it is finished? Is there a configuration element I'm missing? David Hoover Helix Systems Staff http://helix.nih.gov

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building NGS indexes on user sequences
by Michael Pheasant 01 Dec '10

01 Dec '10

Hi We want to allow users to index sequences in galaxy (for example in the data libraries) for use with NGS tools (Bowtie, BWA, etc). Has anyone made tools for NGS indexing? It will also require changing the .loc files for the NGS tools & dynamic re-configuring of tools, which is all possible. Users might want to index & map reads to either their own sequences or other sequences that arent available in the default list, and this would remove the need for admin intervention. Any one else doing something similar? Or can it be done now & I just dont see it? Cheers, Mike.

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cleaning old data set
by Vipin TS 01 Dec '10

01 Dec '10

Dear Galaxy team, With reference to the document sited at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDat…, I tried to clean up old dataset from our Galaxy instance. For example: deleting the userless histories based on the time span, the clean up scripts run perfectly but the dataset is not removed from the disk. Thanks for your support, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824

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Re: [galaxy-dev] [galaxy-user] Data Library Import "tool error"
by Sridhar A Malkaram 30 Nov '10

30 Nov '10

Thanks Nate, I couldn't find a logfile in the galaxy-dist directory.Where is it located? However, when I redid the library upload operation it did not produce any errors. I believe, it my mistake in uploading. The files were located on an nfs server, which is somewhat slow, and I have migrated to another page before the library upload was complete. I thought the process would get completed in background and navigated away to another page. This time, I waited till the process was complete. There were no errors. Thanks. -- With Regards, Sridhar ----- Message from nate(a)bx.psu.edu --------- Date: Tue, 30 Nov 2010 16:27:19 -0500 From: Nate Coraor <nate(a)bx.psu.edu> Reply-To: Nate Coraor <nate(a)bx.psu.edu> Subject: Re: [galaxy-user] Data Library Import "tool error" To: Sridhar A Malkaram <smalkaram2(a)unl.edu> Cc: Galaxy Dev <galaxy-dev(a)bx.psu.edu> > Sridhar A Malkaram wrote: >> >> >> Hi, >> >> I used the "Upload files from filesystem paths" option to upload a >> directory path into Galaxy Data library. I used the option NO for >> "Copy data into Galaxy?" as I don't want a duplicate copy of the >> data. I selected the hg19 for Genome. After the upload process is >> finished, I can see the directory tree structure, but in the >> "information" column for files, it reports "Job error (click name >> for more info)". >> >> When I click a file, for example for "macs_test_1_out.bed", which >> is a bed filetype, it says "failure running job tool error" under >> "Miscellaneous information". I am pasting below the whlole >> information. >> >> This happens for all the data files that are uploaded. What is >> this error? and which tool it is complaining about? > > Hi Sridhar, > > Since this question concerns a local installation of Galaxy, I've moved > it over to the galaxy-dev list. > > Is there anything displayed in Galaxy's server log when this failure > occurs? > >> My another question is, can we upload files/directories with >> compressed format files (.tar, .gz, .bz. etc) and binary files like >> .doc, .xls ? If so, what additional plugins we need to have in >> place? > > Single-file zip and tar(.gz or .bz2) files can be uploaded, as well as > directly compressed .gz and .bz2 files. All of these, however, will be > decompressed upon uploading. > > I believe someone made a datatype for .xls, but it is not part of the > Galaxy distribution. > > --nate > >> >> Thanks in advance for your suggestions. >> >> ================================ Message: >> >> Galaxy Test-data Uploaded by: Date uploaded: 2010-11-29 >> File size: 52.2 Kb Data type: data Build: hg19 Miscellaneous >> information: failure running job tool error Database/Build: hg19 >> Peek: >> >> Disk file: >> /mnt/bioinfo/LINKS/Biotin/data/work/galaxy-dist/test-data/peakcalling_macs/macs_test_1_out.bed >> >> ================================ >> >> -- >> With Regards, >> >> Sridhar >> Postdoctoral Research Associate >> Nutrition and Health Sciences >> University of Nebraska-Lincoln >> >> > >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user[1] > ----- End message from nate(a)bx.psu.edu ----- Links: ------ [1] http://lists.bx.psu.edu/listinfo/galaxy-user

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Re: [galaxy-dev] [galaxy-user] Data Library Import "tool error"
by Nate Coraor 30 Nov '10

30 Nov '10

Sridhar A Malkaram wrote: > > > Hi, > > I used the "Upload files from filesystem paths" option to upload a > directory path into Galaxy Data library. I used the option NO for > "Copy data into Galaxy?" as I don't want a duplicate copy of the > data. I selected the hg19 for Genome. After the upload process is > finished, I can see the directory tree structure, but in the > "information" column for files, it reports "Job error (click name > for more info)". > > When I click a file, for example for "macs_test_1_out.bed", which > is a bed filetype, it says "failure running job tool error" under > "Miscellaneous information". I am pasting below the whlole > information. > > This happens for all the data files that are uploaded. What is > this error? and which tool it is complaining about? Hi Sridhar, Since this question concerns a local installation of Galaxy, I've moved it over to the galaxy-dev list. Is there anything displayed in Galaxy's server log when this failure occurs? > My another question is, can we upload files/directories with > compressed format files (.tar, .gz, .bz. etc) and binary files like > .doc, .xls ? If so, what additional plugins we need to have in > place? Single-file zip and tar(.gz or .bz2) files can be uploaded, as well as directly compressed .gz and .bz2 files. All of these, however, will be decompressed upon uploading. I believe someone made a datatype for .xls, but it is not part of the Galaxy distribution. --nate > > Thanks in advance for your suggestions. > > ================================ Message: > > Galaxy Test-data Uploaded by: Date uploaded: 2010-11-29 > File size: 52.2 Kb Data type: data Build: hg19 Miscellaneous > information: failure running job tool error Database/Build: hg19 > Peek: > > Disk file: /mnt/bioinfo/LINKS/Biotin/data/work/galaxy-dist/test-data/peakcalling_macs/macs_test_1_out.bed > > ================================ > > -- > With Regards, > > Sridhar > Postdoctoral Research Associate > Nutrition and Health Sciences > University of Nebraska-Lincoln > > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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error uploading file into Library
by Glen Beane 30 Nov '10

30 Nov '10

I'm trying to upload a 26GB BAM file into a shared library in our private Galaxy instance. I've tried at least 5 times with both the "Upload directory of files" and "Upload from filesystem path" options. I keep getting an error like this: uploaded bam fileTraceback (most recent call last): File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 414, in __main__() File "/galaxydata/galaxy-setup/galaxy-dist/tools/data_source/upload.py", line 406, in __m error I haven't had any problems like this before, but this is the largest file I've tried to load into Galaxy. Any suggestions on how to debug this? -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

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Error following update: unknown locale 'en_GB'
by Chris Cole 30 Nov '10

30 Nov '10

Hi, I've just updated our local Galaxy install and got an error when trying to run it. It started fine, but as soon as I tried to connect with Firefox it brought up a server error: 10.31.3.203 - - [12/Nov/2010:12:07:05 +0100] "GET / HTTP/1.1" 500 - "-" "Mozilla/5.0 (X11; Linux i686; rv:2.0b7) Gecko/20100101 Firefox/4.0b7" Error - <class 'babel.core.UnknownLocaleError'>: unknown locale 'en_GB' URL: http://xxxxxxxxxxxxx/ File '/homes/www-galaxy/galaxy_devel/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/homes/www-galaxy/galaxy_devel/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/homes/www-galaxy/galaxy_devel/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/base.py', line 119 in __call__ trans = self.transaction_factory( environ ) File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 161 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 181 in transaction_chooser return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 785 in __init__ GalaxyWebTransaction.__init__( self, environ, app, webapp ) File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 193 in __init__ self.setup_i18n() File '/homes/www-galaxy/galaxy_devel/lib/galaxy/web/framework/__init__.py', line 204 in setup_i18n locales = [ Locale.parse(l.split( ';' )[0], sep='-').language for l in locales ] File '/homes/www-galaxy/galaxy_devel/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 212 in parse File '/homes/www-galaxy/galaxy_devel/eggs/Babel-0.9.4-py2.6.egg/babel/core.py', line 137 in __init__ UnknownLocaleError: unknown locale 'en_GB' Strangely, /homes/www-galaxy/galaxy_devel/eggs/Babel-0.9.4-py2.6.egg/babel/core.py doesn't exist? Any pointers on how to fix this? Cheers, Chris

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database_connection string format
by Marina Gourtovaia 30 Nov '10

30 Nov '10

Hello I am new to Galaxy. Trying to set up a server locally and back it up with mysql database. What is the right format for the database_connection string in the universe_wsgi.ini file? I understand that it should be something like this: mysql://user:password@host/dbname[?key=value..] Where the port number should go? Marina Gourtovaia -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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bigWig display at UCSC
by Brad Chapman 30 Nov '10

30 Nov '10

Hi all; We're having trouble displaying BigWigFiles at UCSC and are getting error messages from UCSC like: http://main.g2.bx.psu.edu/display_application/238cdead8fb6f8fe/ucsc_bigwig/… is not a chromosome id r-tree index file I see the same issue on Galaxy main, which can be replicated by trying to view the test.bigwig file from this history: http://main.g2.bx.psu.edu/u/Brad%20Chapman/h/imported-test-history-for-chap… We noticed the problem after an upgrade to the latest galaxy-central on Friday, but I haven't been able to track down any changes which seem to be causing it. Other display types (BAM, regular wiggle) work fine. Does anyone know of recent changes to display applications which might be causing this? Any directions to dig into would be appreciated. Thanks much, Brad

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PyPy Status Blog: PyPy 1.4: Ouroboros in practice
by Davide Cittaro 30 Nov '10

30 Nov '10

Anybody tested this? http://morepypy.blogspot.com/2010/11/pypy-14-ouroboros-in-practice.html 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 */

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galaxy-dev November 2010