August 2010 - galaxy-dev - lists.galaxyproject.org

Getting genomes into a standalone galaxy instance
by Will Dampier 11 Aug '10

11 Aug '10

I've been trying to get genomes into my local galaxy instance to use the "Fetch Sequences - Extract Genomic DNA" tool. I've read plenty of posts about adding custom genomes but I'm just looking to download the standard genomes already included with Galaxy, ie. mm9, hg19, etc. I've already run the updateucsc.sh which created the indexes however, I need to download the actual genome sequences and put them where Galaxy can find them. I'm sure I'm missing a command somewhere. Thanks for the help. Dr. Will Dampier Instructor, Drexel University Assistant Director, Center for Integrated Bioinformatics, School of Biomedical Engineering and Health Systems, Bossone 714, Drexel University, 3143 Chestnut St, Philadelphia, PA 19104

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Re: [galaxy-dev] Server error from history view
by simon andrews (BI) 11 Aug '10

11 Aug '10

Yes, definitely using galaxy central. The command I used earlier today was: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_central Do I need to do anything else to pull in your latest additions? Simon. -----Original Message----- From: James Taylor [mailto:james@jamestaylor.org] Sent: 10 August 2010 16:14 To: simon andrews (BI) Subject: Re: [galaxy-dev] Server error from history view Hi Simon, it looks like you are still running an older revision there (paste translogger should no longer appear in the stack trace). I may have done something wrong, but just wanted to check first that you are sure this is from galaxy-central. Thanks! On Aug 10, 2010, at 11:08 AM, simon andrews (BI) wrote: > James, > > Sorry to take so long to follow up on this. I've installed an > instance of galaxy_central and have replicated the problem I had in > galaxy_dist. I get the same internal server error in the history > view and the backtrace I get in the console is below. > > I hope this is a little more informative in getting to the bottom of > this problem. As before, the error only occurrs when debugging is > disabled. With debugging enabled the server runs normally. > > Simon. > > Exception happened during processing of request from > ('149.155.147.76', 50098) > Traceback (most recent call last): > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line > 1068, in > pro > cess_request_in_thread > self.finish_request(request, client_address) > File "/usr/lib64/python2.6/SocketServer.py", line 320, in > finish_request > self.RequestHandlerClass(request, client_address, self) > File "/usr/lib64/python2.6/SocketServer.py", line 615, in __init__ > self.handle() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line > 442, in > hand > le > BaseHTTPRequestHandler.handle(self) > File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle > self.handle_one_request() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line > 437, in > hand > le_one_request > self.wsgi_execute() > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line > 287, in > wsgi > _execute > self.wsgi_start_response) > File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, > in __call__ > return app(environ, start_response) > File "/data/private/galaxy/galaxy_central/lib/galaxy/web/framework/ > middleware > / xforwardedhost > .py", line 21, in __call__ > return self.app( environ, start_response ) > File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", > line 164, in > _ > _call__ > app_iter = self.application(environ, start_response) > File "/usr/lib/python2.6/site-packages/paste/translogger.py", line > 68, in > __ca > ll__ > return self.application(environ, replacement_start_response) > File "/usr/lib/python2.6/site-packages/paste/exceptions/ > errormiddleware.py", > l > ine > 154, in __call__ > exc_info) > File "/usr/lib/python2.6/site-packages/paste/translogger.py", line > 67, in > repl > acement_start_response > return start_response(status, headers) > File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line > 166, in > wsgi > _start_response > assert 0, "Attempt to set headers a second time w/o an exc_info" > AssertionError: Attempt to set headers a second time w/o an exc_info > ---------------------------------------- > > -----Original Message----- > From: James Taylor [mailto:james@jamestaylor.org] > Sent: 04 August 2010 20:19 > To: simon andrews (BI) > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Server error from history view > > Hi Simon, > > The problem that was masking real exceptions when debug mode was *off* > is now fixed in galaxy-central. Thus, you should see a real exception > in the logs if you try again. If you test this, could you let us know > what the exception is? It is very odd that you don't see any exception > in the UI when debug is on. It might be occurring in an asynchronous > request that is not visible or something else unusual. > > Thanks > James > > -- jt > > James Taylor > Assistant Professor > Department of Biology > Department of Mathematics & Computer Science > Emory University > > On Aug 3, 2010, at 6:56 AM, simon andrews (BI) wrote: > >> Having gone back to a stock configuration this error went away. >> Having reapplied all of my changes one at a time the one which >> causes the problem is disabling debug mode in universe_wsgi.ini. If >> I add >> >> debug = False >> >> to the config (removing the original), then I get the error below. >> If I leave debugging on then the histories work again. >> >> Simon. >> >> -----Original Message----- >> From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu >> ] On Behalf Of simon andrews (BI) >> Sent: 30 July 2010 15:44 >> To: galaxy-dev(a)bx.psu.edu >> Subject: [galaxy-dev] Server error from history view >> >> I'm making pretty good progress setting up our galaxy server, but >> have hit a snag. Since moving from an SQLite to a MySQL backend I'm >> getting an internal server error from the history panel on our >> galaxy instance. Running the galaxy server from a console gives me >> the following python traceback: >> >> ---------------------------------------- >> Exception happened during processing of request from ('127.0.0.1', >> 60795) >> Traceback (most recent call last): >> File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line >> 1068, in process_request_in_thread >> self.finish_request(request, client_address) >> File "/usr/lib64/python2.6/SocketServer.py", line 320, in >> finish_request >> self.RequestHandlerClass(request, client_address, self) >> File "/usr/lib64/python2.6/SocketServer.py", line 615, in __init__ >> self.handle() >> File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line >> 442, in handle >> BaseHTTPRequestHandler.handle(self) >> File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle >> self.handle_one_request() >> File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line >> 437, in handle_one_request >> self.wsgi_execute() >> File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line >> 287, in wsgi_execute >> self.wsgi_start_response) >> File "/usr/lib/python2.6/site-packages/paste/urlmap.py", line 203, >> in __call__ >> return app(environ, start_response) >> File "/data/private/galaxy/galaxy_dist/lib/galaxy/web/framework/ >> middleware/xforwardedhost.py", line 21, in __call__ >> return self.app( environ, start_response ) >> File "/usr/lib/python2.6/site-packages/paste/deploy/config.py", >> line 164, in __call__ >> app_iter = self.application(environ, start_response) >> File "/usr/lib/python2.6/site-packages/paste/translogger.py", line >> 68, in __call__ >> return self.application(environ, replacement_start_response) >> File "/usr/lib/python2.6/site-packages/paste/exceptions/ >> errormiddleware.py", line 154, in __call__ >> exc_info) >> File "/usr/lib/python2.6/site-packages/paste/translogger.py", line >> 67, in replacement_start_response >> return start_response(status, headers) >> File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line >> 166, in wsgi_start_response >> assert 0, "Attempt to set headers a second time w/o an exc_info" >> AssertionError: Attempt to set headers a second time w/o an exc_info >> ---------------------------------------- >> >> Any ideas? >> >> Thanks >> >> Simon. >> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> _______________________________________________ >> galaxy-dev mailing list >> galaxy-dev(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-dev > > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-dev

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Passing a file and the contents in file.files_path
by Roger Kapul 10 Aug '10

10 Aug '10

Hello, I was wondering if it was possible to pass a file and that files contents to another tool in a workflow. Currently I have a tool that creates an html file with an embedded image. When passing the html file into the next step in the workflow, that aggregates all the outputs from the various steps into another html file, clicking on the link in the aggregated html file only renders the html of the original file without the embedded image. So I guess my main question is would it be possible pass a file and it's contents, without zipping everything and transferring as a .zip? Thanks for your help, Roger

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Workflow not "flowing"
by Marijn Vandevoorde 10 Aug '10

10 Aug '10

Hi all, I'm setting up our own galaxy service here, but I've run into a rather basic problem: whenever my first step finishes, it just stops there. The second job in my history just keeps waiting forever and I really don't know why. Here's the workflow: input dataset -> FASTQ Groomer (until here ok) -> Map With BWA (together with a reference dataset of course). And there it just stops. When I try to edit the BWA, it complains a bit about missing meta data: Required metadata values are missing. Some of these values may not be editable by the user. Selecting "Auto-detect" will attempt to fix these values. Adding a step action to change the datatype of the outputfile to fastqsanger doesn't help either. Any ideas? Let me know if you need more info! Thanks! Marijn

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Galaxy on Mac OS
by sohkhan＠notes.cc.sunysb.edu 10 Aug '10

10 Aug '10

Hi, I am wondering if it is possible to run Galaxy on a MacPro? Sorry I am new to Mac..........been using it for last 2 days. Thanks. -Sohail

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Downloading datasets
by SHAUN WEBB 09 Aug '10

09 Aug '10

Hi, is it possible, when downloading datasets from a Galaxy library or saving datasets from a history, for the created files to be named exactly as appears in the library without the additional "GalaxyLibraryDataset..." prefix. Thanks Shaun webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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<filter> tag in output
by Davide Cittaro 09 Aug '10

09 Aug '10

Hi all, Apparently I cannot have the <filter> tag working for outputs in the small tool I'm wrinting: <tool id="srf2fastq" name="SRF to FASTQ"> <description>conversion</description> <command interpreter="sh">srf2fastq.sh $input1 $filter $paired $out_file1 $out_file2 </command> <inputs> <param name="input1" type="data" format="srf" label="Select SRF Archive"/> <param name="filter" label="Filter out bad reads (QC fail)?" type="boolean" truevalue="Y" falsevalue="N" selected="True"/> <param name="paired" label="Is this Paired-end run?" type="boolean" truevalue="Y" falsevalue="N" selected="False"/> </inputs> <outputs> <data format="fastqillumina" name="out_file1"/> <data format="fastqillumina" name="out_file2"> <filter>paired == "Y"</filter> </data> </outputs> […] </tool> According to the wiki pages, this syntax should enable the out_file2 if the "paired" checkbox is clicked... Unfortunately I always have the tool running as the checkbox wasn't checked (i.e. out_file2 is None). If I change the filter condition to paired=="N" I always have the tool running with two outputs... Can anybody help me? thanks 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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Sort tab error?
by Minh Bui 06 Aug '10

06 Aug '10

Hi, I always get this error when I use Sort feature *"An error occurred running this job: sort: multi-character tab `$\t'"* Even I already use Text Manipulation->Convert to convert my table to Tabs format. Here is the screenshot of what happen (I want to sort C2 on job #12) : http://img408.imageshack.us/img408/7906/screenshotbu.png Could someone please show me how to fix this? Thank you.

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strange behavior of display_as
by Davide Cittaro 06 Aug '10

06 Aug '10

Hi there, I may need some help in debugging this: I have added some files to a library, say foo.bed. I've changed (as admin) the name from "foo.bed" to "the foo dataset". I've imported this into my current history and if I try to visualize this bed file on the genome browser, I get this error: http://host001.instruments.ifom-ieo-campus.it:8080/root/display_as?id=213&d…: 404 Not Found (host001 is the galaxy server). If I download "the foo dataset" and reupload it to galaxy, the "display_as" doesn't work (same error). Strange enough, if I import a bed file from the genome browser (say some chrom.refseq.bed) I can visualize it back (so "display_as" is working). No strange logs... 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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feature request
by Davide Cittaro 06 Aug '10

06 Aug '10

Hi there, I'm manually editing some files in my data library and I've figured out a couple of feature that (IMHO) are missing: - possibility to copy/move a file from a library to another (or in a folder hierarchy) - a display of the full filesystem path of the referenced file (in the admin view, of course) 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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