- galaxy-dev - lists.galaxyproject.org

Fwd: Galaxy crach while visualization
by Chebbi Mohamed Amine 25 Jul '12

25 Jul '12

---------- Forwarded message ---------- From: Chebbi Mohamed Amine <chebbimamine(a)gmail.com> Date: 2012/7/18 Subject: Re: [galaxy-dev] Galaxy crach while visualization To: Jeremy Goecks <jeremy.goecks(a)emory.edu> Hello Jeremy! Thanks for your response. Yes the paster.log is not complaining. Excuse me where I can found the javascript log. In /var/log I haven't any file related to javascript.log. Thanks Amine 2012/7/17 Jeremy Goecks <jeremy.goecks(a)emory.edu> > Hello Amine, > > The paster log looks normal, and Postgre log is standard given the crash. > Was there anything out of the ordinary that you can spot in the paster log > and/or Javascript log in your Web browser? > > Thanks, > J. > > On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote: > > Hello Galaxy team ! > > I have e strange problem whith my Galaxy trackster visualization . While > viewing bookmarked regions in my visualisation the whole > Galaxy process crashed and needed to be restarted, mainly when I use > Chrome browser. > > Above the Paster.log : > > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=f4b17be90d9b3c9d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1183972&high=1185154&mode=Auto&resolution=2.954022988505747&dataset_id=ec90add676cb0cce&hda_ldda=hda&filter_cols=%5B%22Mapping+Quality%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1180427&high=1181609&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1181609&high=1182791&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) > AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=1182790&high=1183972&mode=Auto&resolution=2.954022988505747&dataset_id=cc26e7b927e75a3d&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] "GET > /galaxy/tracks/data?chrom=chr19&low=814128&high=815310&mode=Auto&resolution=2.954022988505747&dataset_id=7710e7c5028b7c3b&hda_ldda=hda&filter_cols=%5B%22Score%22%5D > HTTP/1.1" 200 - " > http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output" > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, > like Gecko) Chrome/20.0.1132.47 Safari/536.11" > > PostgreSQL saw the crach : > > 2012-07-12 12:56:40 CEST LOG: could not receive data from client: > Connection reset by peer > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:00:46.907 > user=user database=database host=server port=33106 > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:03:45.206 > user=user database=database host=server port=42867 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:06:43.257 > user=user database=database host=server port=56383 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.120 > user=user database=database host=server port=42663 > 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.596 > user=user database=database host=server port=42656 > > > Thanks > Amine > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > >

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.loc file for tophat
by Andre Gatorano 25 Jul '12

25 Jul '12

Which .loc file corresponds to tophat? I looked through the .xml file for the wrapper and it made no reference to any .loc file. -- Andre Gatorano 847-845-9284 University of California San Diego

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Populating tool select menu with database data? <code> tag deprecated
by Kohler Manuel 25 Jul '12

25 Jul '12

Hi, I have a question related to this Galaxy threads: http://dev.list.galaxyproject.org/Populating-tool-select-menu-with-database -data-tp4139069.html I implemented the example with the deprecated <code> tag which is working fine. But I do not invest time in a tag which might vanish soon. What is the replacement for this tag or how is the way it should be done? Here is what I want to do: My ultimate goal is to load fastq.gz files from an external Data Management System which I can connect via a JSON API. Here is the code which generates the menu shwon in the attached screen shot: Python code: import jsonrpclib server = jsonrpclib.Server('https://<myserver>/rmi-general-information-v1.json') sessionToken = server.tryToAuthenticateForAllServices(<user>, <password>) projects = server.listProjects(sessionToken) experimentType = 'HT_SEQUENCING' def getExperiments(): eList = [] experiments = server.listExperiments(sessionToken, projects, experimentType) for experiment in experiments: eList.append([experiment['code'], experiment['code'], False]) return eList The corresponding XML file calls the getExperiments() function: <inputs> <param name="experiment" type="select" label="Experiment:" help="select Experiment" dynamic_options="getExperiments()"/> <outputs> <data format="fasta" name="output" label="more foo" /> </outputs> <code file="openbis_get_dataset.py" /> Depending on the selection in the first drop down list (experiments) I want to show/fill a second list which shows a list of items which are in the selected experiment. Finally the fastq files should be listed. The structure is like this: *Experiment1 - Sample1 + fastq1.gz + fastq2.gz + fastq3.gz - Sample2 + fastq1.gz + fastq2.gz *Experiment2 - Sample1 + fastq1.gz I am on Galaxy r7148. If somebody could direct me in the right direction would be highly appreciated. Kind regards Manuel -- Manuel Kohler Center for Information Sciences and Databases (C-ISD) Department of Biosystems Science & Engineering (D-BSSE) ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132

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Local instance is running way too slow!!!
by Di Nguyen 25 Jul '12

25 Jul '12

Dear All, I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I tried to use Galaxy, it is painfully slow! The first test I did was to create Admin and import data (RNA-seq fastq, about 6Gb in size) into database and then history and it worked fine. The second test was to run fasqgroomer on this fasq and it took forever (3 hours+). Anybody got in idea of why it is so slow? Would it be possible that Galaxy was set up to run a single process instead of 8-core processor? If that is the case, how to fix it? Please help! Di Nguyen Postdoc, U of W, Seattle, WA

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Build indexes for BWA, Bowtie, and others in local instance
by Di Nguyen 25 Jul '12

25 Jul '12

Dear all, I just installed my local instance. In order to use NGS tools, I need indexes. Do I have to build these indexes species by species, program by programs or there is a SHORTCUT for Galaxy compatible readied for download indexes? If I'am not mistaken, building these indexes can take weeks? Kindest regards, Di

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Local Instance is running way too slow!!!
by Di Nguyen 24 Jul '12

24 Jul '12

Dear All, I successfully install Galaxy onto my new MBP with 16Gb or Ram but when I tried to use Galaxy, it is painfully slow! The first test I did was to create Admin and import data (RNA-seq fastq, about 6Gb in size) into database and then history. The second test was to run fasqgroomer on this fasq and it took forever (a couple of hours and still running). Anybody got in idea of why it is so slow? Would it be possible that Galaxy was set up to run a single process instead of 8-core processor? If that is the case, how to fix it? Please help! Di Nguyen Postdoc, U of W, Seattle, WA

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loading bam file to galaxy
by Maya Abraham-Malaev 24 Jul '12

24 Jul '12

Hello, I'm running a local installation of galaxy. While loading a bam file (2GB) to galaxy, I get the following error: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 403, in <module> __main__() File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File "/home/galaxy/galaxy-dist/tools/data_source/upload.py", line 331, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/home/galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1220, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory I've succeeded to execute other commands that used samtools. I've also succeeded in running the command: subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] in python on the server which galaxy installed on, logged in to the user under which galaxy is executed. Do you have any idea what can cause it, and how to solve the problem? Maya

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PBSpro Cluster Server possible?
by Stephan Frickenhaus 24 Jul '12

24 Jul '12

Hello, I have tried to couple our GALAXY-server (unified, running on a virtual server, ubuntu 12) with our big SGI Cluster-Server uv100 running PBSpro as job system (pbs_version = PBSPro_11.1.1.112253). On the GALAXY-server I have installed ii pbs-drmaa-dev 1.0.10-2 DRMAA for Torque/PBS Pro - devel ii pbs-drmaa1 1.0.10-2 DRMAA for Torque/PBS Pro - runtime We have the GALAXY-sources installed very recently; job-creation is prepared, but no job is scheduled to our uv100. Did you ever hear that the libdrmaa.so coming with this package is useful to couple to a PBSpro-server? The DRMAA_LIBRARY_PATH has been set accordingly to /usr/lib/libdrmaa.so.1.0.10 . we set default_cluster_job_runner = drmaa://uv100.awi.de/slong/ We also checked that the torque-system on the GALAXY-Server could successfully submit jobs by "qsub" on the PBSpro-server in the slong queue. Best regards and many thanks in advance, S. Frickenhaus -- -- Prof. Dr. Stephan Frickenhaus Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631 Alfred-Wegener-Institut f. Polar- u. Meeresforschung Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus(a)awi.de 0471-4831-1179 0151-1741 1631 -- Prof. Dr. Stephan Frickenhaus FB1 - Biotechnologie Hochschule Bremerhaven An der Karlstadt 8 27568 Bremerhaven 0471-4823-525 0151-1741 1631 Alfred-Wegener-Institut f. Polar- u. Meeresforschung Bioinformatik/Rechenzentrum Am Handelshafen 12 27570 Bremerhaven stephan.frickenhaus(a)awi.de 0471-4831-1179 0151-1741 1631

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Multiple .CEL file import for microarray analysis
by Jon Manning 23 Jul '12

23 Jul '12

Hi all, My apologies if this seems obvious to many of you (seems like something that will have been dealt with)- but I've been rooting around in the docs and mailing list to no concrete avail. I'm looking to Galaxyise our existing (somewhat informal) microarray analysis workflows. I've found rexpression etc and the associated helpful datatypes. But I'm stuck at the import of .CEL files: * Do I need to create a new datatype to represent .CEL? The fact this doesn't exist by default suggests it's not the right approach. * Assuming I was to do the above, how would I create a function to generate an affyBatch (for example) from an unspecified number of input .CEL? * Is the solution to have R work with a .tar and a config file to produce the affyBatch, thereby bypassing the .CEL requirement? But then there's no .tar datatype either..... If I've missed the docs I'm happy to be chided and pushed in the right direction. Many thanks, Jon -- Dr Jonathan Manning Bioinformatics Team Centre for Cardiovascular Science University of Edinburgh Queens Medical Research Institute 47 Little France Crescent Edinburgh EH16 4TJ United Kingdom T: +44 131 242 6700 F: +44 131 242 6782 E: jmanning(a)staffmail.ed.ac.uk The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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dns lookup failure and proxy errors from internal toolshed?
by Smithies, Russell 23 Jul '12

23 Jul '12

I'm trying to setup an internal toolshed but am getting DNS and proxy errors: (I'm using port 8081 instead of 9009) The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /toolshedrepository/browse_valid_repositories<http://galaxy-dev.agresearch.co.nz/toolshedrepository/browse_valid_reposito…>. Reason: DNS lookup failure for: localhost:8081repository I'm rewriting my URLs like this: RewriteRule ^/toolshed$ /toolshed/ [R] RewriteRule ^/toolshed/static/style/(.*) /var/lib/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule ^/toolshed/static/scripts/(.*) /var/lib/galaxy/static/scripts/packed/$1 [L] RewriteRule ^/toolshed/static/(.*) /var/lib/galaxy/static/$1 [L] RewriteRule ^/toolshed/favicon.ico /var/lib/galaxy/static/favicon.ico [L] RewriteRule ^/toolshed/robots.txt /var/lib/galaxy/static/robots.txt [L] RewriteRule ^/toolshed(.*) http://localhost:8081$1 [P] I think it might be an Apache problem but no idea hat to try next. Any ideas? Thanx, Russell Smithies Invermay Agricultural Centre Puddle Alley, Private Bag 50034, Mosgiel 9053, New Zealand T +64 3 489 3809 F +64 3 489 3739 www.agresearch.co.nz<http://www.agresearch.co.nz/> ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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