March 2013 - galaxy-dev - lists.galaxyproject.org

Bam to sam error
by Joachim Jacob | VIB | 08 Mar '13

08 Mar '13

Hello, I got an error on our local Galaxy using bam-to-sam. The BAM file is a result of a Tophat version 1 run. The error Error sorting alignments from (/mnt/galaxydb/files/006/dataset_6733.dat), error An error occurred with this dataset:/Samtools Version: 0.1.18 (r982:295) Error sorting alignments from (/mnt/galaxydb/files/006/dataset_6733.dat),/ Thanks for the assistance, 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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Include some XML in <configfiles> tag
by David Angot 08 Mar '13

08 Mar '13

Hello, I have a tool that takes an XML file as input. So I thought it would be a good idea to put it in the <configfiles> tag, to replace some of the variables. Quick example : .... <inputs> <param name="posfile" type="data" label="Posfile" help="Posfile you want to input to POSGEN" format="pos" /> </inputs> <configfiles> <configfile name="loadTestxml"> <!DOCTYPE crystal SYSTEM "/usr/share/sgml/crystal.dtd">  <crystal> <version value="0.0.1"/> <posload name="${posfile}"/> </crystal> </configfile> </configfiles> .... But when I load the tool configuration, it seems that the XML in <configfile> is interpreted, and/or I don't get anything in the input file. Is there a way to do what I want ? Cheers, -- David

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FTP uploading errors and BigWig conversion
by Kristin Denise Kernohan 08 Mar '13

08 Mar '13

Hello I have been dealing with 2 problems for several weeks and am hoping you can provide assistance: #1 - File uploads seem to be very inconsistent. I am using an FTP server, the files upload to the FTP fine - but when I assign them to upload in Galaxy, they often enter a que which I have let run for up to a week and they do not transfer. If I keep restarting it then sometimes they will transfer in a minute, while the same file will enter a que and not transfer minutes later. The files I am using are fairly small (20MB) so I cannot see why there are so many difficulties uploading them. #2- The Bedgraph/Wig to BigWig conversion tool - is it normal for this to take 1.5-2 weeks to run? Every once and awhile I get lucky and it runs in ~12 hours, but other files started at the same time are taking up to 2 weeks to convert. I greatly appreciate any advice you can provide to rectify these situations Kristin Kernohan

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API - Status 403 Forbidden
by Rob Leclerc 08 Mar '13

08 Mar '13

I'm trying to use the blend4j to access the Galaxy API, but I'm getting a 403 error, however when I pass the same request string through my browser I get a json response (Status 200). //Here is the URL string being passed in both cases: http://localhost:8080/api/histories?key=c5954f0e726e52da297cdad5ad4aa249 //Below are the Galaxy logs emitted on my localhost: 127.0.0.1 - - [07/Mar/2013:21:12:01 -0400] "GET /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.22 (KHTML, like Gecko) Chrome/25.0.1364.155 Safari/537.22" 127.0.0.1 - - [07/Mar/2013:21:12:24 -0400] "GET /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1" 403 - "-" "Java/1.6.0_41" I'm not sure if this is related or not, because I can logout in my browser and still hit the local server without getting a 403, but how do I login (and logout) through the API to set up a session because I assume that the API key is only valid for the logged in user? Is there an API request for the login? Cheers, Rob

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upload of local file ends up with a broken pipe.
by Jason Evans 07 Mar '13

07 Mar '13

I am having difficulties with my local instance of Galaxy on Mac OS X. Upon using the local file upload tool I get an error resultant of a broken pipe in python. The command-line output is as follows. 127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] "GET /history HTTP/1.1" 500 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50438) Traceback (most recent call last): File "/Users/jjevans/Work/Tools/Galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler 'upload_handler' My instance has worked for this task in the past, but I'm not sure if it has been since my last Galaxy update or perhaps something with my configuration changed. thanks for your help, Jason

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Tools and Data
by shenwiyn 07 Mar '13

07 Mar '13

Hi, I have some questions about the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gz....I don't know the differents among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174. Could anyone help me and give me some advice please? Thank you very much. shenwiyn

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Please help with fastx broken pipe
by Jorge Sepulveda 07 Mar '13

07 Mar '13

Hi, Fresh new installation of galaxy on a MacPro 12 core Mountain Lion Trying to run fastx_quality_stats: galaxy.jobs.manager DEBUG 2013-01-16 16:03:49,646 (7) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-01-16 16:03:54,759 (7) Working directory for job is: /Users/JS/galaxy-dist/database/job_working_directory/000/7 galaxy.jobs.handler DEBUG 2013-01-16 16:03:54,759 dispatching job 7 to local runner galaxy.jobs.handler INFO 2013-01-16 16:03:54,854 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:54,919 Local runner: starting job 7 galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,198 executing: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs.runners.local DEBUG 2013-01-16 16:03:55,396 execution finished: cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_7.dat' galaxy.jobs DEBUG 2013-01-16 16:03:55,440 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-01-16 16:03:55,496 setting dataset state to ERROR galaxy.tools DEBUG 2013-01-16 16:03:55,618 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/JS/galaxy-dist/database/job_working_directory/000/7/galaxy.json' galaxy.jobs DEBUG 2013-01-16 16:03:55,679 job 7 ended 127.0.0.1 - - [16/Jan/2013:16:03:59 -0400] "GET /history HTTP/1.1" 200 - "http://127.0.0.1:8080/root" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" Galaxy reports the following error: /bin/sh: fastx_quality_stats: command not found cat: stdout: Broken pipe When run on the cmd line, it runs fine: $ cat '/Users/JS/galaxy-dist/database/files/000/dataset_2.dat' | fastx_quality_stats -Q 33 -o '/Users/JS/galaxy-dist/database/files/000/dataset_6.dat' $ more /Users/JS/galaxy-dist/database/files/000/dataset_6.dat column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count 1 912999 7 46 31022469 33.98 32 35 37 5 25 44 153534 361457 322516 75492 0 912999 2 912999 3 46 29744797 32.58 31 34 36 5 24 43 316245 255564 197711 143479 0 912999 Jorge Sepulveda, MD, PhD Associate Director for Laboratory Medicine, Medical Director of Laboratory Informatics, Columbia University Medical Center Associate Professor, Department of Pathology & Cell Biology Columbia University College of Physicians and Surgeons PH1590B 622 W 168 St New York, NY 10032 Cell: (917) 862-6050 Office: 212-305-6360 E-mail:jls2282@columbia.edu

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Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013
by Jennifer Jackson 07 Mar '13

07 Mar '13

Notice Date: Thursday, March 7, 2013 Greetings Galaxy *Main* & *Test* Users, The *Galaxy* *Public* *Main Galaxy Server <http://wiki.galaxyproject.org/Main>* at *http://main.g2.bx.psu.edu* (/usegalaxy.org/) and *Test Galaxy Server <http://wiki.galaxyproject.org/Test>* at *http://test.g2.bx.psu.edu* will be *down on Thursday, March 14, while the team _/relocates core hardware /to a new server room_*. Please note that _/ALL jobs running at the time of the shutdown will be terminated/_. Once the move is complete, any terminated jobs can be easily restarted using the "re-run" function. dataset re-run The /yellow banner on //*Main*//and //*Test*//will provide updates/ (when the servers are up) as well our *@galaxyproject Twitter* posts. Don't use Twitter? See our *Twitter Wiki <http://wiki.galaxyproject.org/Galaxy%20on%20Twitter>*. *Galaxy's **Tool Shed <http://toolshed.g2.bx.psu.edu>**, **GalaxyProject.org <http://wiki.galaxyproject.org>**Wiki, and **Mailing list <http://wiki.galaxyproject.org/MailingLists>**services* will be /*unaffected*/ during this time. /Thanks for using Galaxy!!/ Galaxy team

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Galaxy Reports: 'unfinished jobs' seems not to do the job
by Joachim Jacob | VIB | 07 Mar '13

07 Mar '13

Hi all, I make increasingly use of the Galaxy Reports tool. Until recently I started it and shut it down again. Now I run it continuously. I have noticed that a lot of the jobs listed in 'unfinished jobs' are actually finished. Any hint on how to clean up the database? Which table? Perhaps I can make a Trello card: 'Provide a button to remove the jobs from the unfinished jobs page' ? Thanks for taking me further, 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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Installing htseq-count via Toolshed: error installing dependency.
by Joachim Jacob | VIB | 07 Mar '13

07 Mar '13

Hi all, Installing htseq-count with dependencies fails on my system: htseq-count installs four dependencies (numpy, picard, samtools, htseq) , of which one fails (htseq), strangely enough. The error is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-856.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). The /apps directory is completely owned by Galaxy. I tried to create that missing directory (reported above), but got a little stuck, since uninstalling the dependency removed that directory again. The tool created the folder /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e with contents: INSTALLATION.log lib Next I looked to the tool_dependency.xml, but with my limited experience did not see something obvious. Thanks for any hint, (prefer to get the installation working from the toolshed) 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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