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

How to configure and set up the Circos on my local Galaxy?
by shenwiyn 11 Sep '13

11 Sep '13

Hi , I found that the visualization of Circos works greatly in Galaxy main,but failed on my local Galaxy.I want to find out some information about configuring and setting up the Circos on local Galaxy,I saw nothing in http://wiki.galaxyproject.org/New%20Visualization%20Page#Circos_plot_.28aka… .Please any suggestions would be most welcome. shenwiyn

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Mail is not configured for this Galaxy instance.
by shenwiyn 11 Sep '13

11 Sep '13

Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :"Mail is not configured for this Galaxy instance. Please contact an administrator. "Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn

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Bismark error
by Nikos Sidiropoulos 11 Sep '13

11 Sep '13

Hi all I installed bismark from the toolshed (bgruening) with all dependencies having been installed successfully and I generated the genomes according to the instructions. While trying to test the tool I got the following error. galaxy.jobs.handler ERROR 2013-09-04 13:14:26,267 Failed to generate job destination Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 287, in __check_if_ready_to_run self.job_wrappers[job.id].job_destination File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 617, in job_destination return self.job_runner_mapper.get_job_destination(self.params) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 163, in get_job_destination self.__cache_job_destination( params ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/jobs/mapper.py", line 148, in __cache_job_destination raw_job_destination = self.job_wrapper.tool.get_job_destination( params ) AttributeError: 'NoneType' object has no attribute 'get_job_destination' galaxy.datatypes.metadata DEBUG 2013-09-04 13:14:26,905 Cleaning up external metadata files galaxy.jobs.handler ERROR 2013-09-04 13:14:27,034 (1316) Error checking job readiness I'm using the old style job configuration (the one in universe_wsgi.ini). Could that be the issue? Bests, Nikos

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Galaxy job status not synchronize with pbs
by Tsung-Ying Tsai 11 Sep '13

11 Sep '13

Hi, I found that there is a problem when pbs job terminate unexpectedly (job killed manually / meet walltime), but galaxy shows the job still working. And there are some error messages from log file below. galaxy.jobs.runners.pbs DEBUG 2013-09-10 18:15:57,841 (3811/762.localhost) PBS job state changed from R to C galaxy.jobs.runners.pbs ERROR 2013-09-10 18:15:57,841 (3811/762.localhost) PBS job failed: Unknown error: -10 galaxy.jobs.runners ERROR 2013-09-10 18:15:57,841 (unknown) Unhandled exception calling fail_job Traceback (most recent call last): File "/mnt/RAID1/mirror/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 58, in run_next method(arg) File "/mnt/RAID1/mirror/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 560, in fail_job if pbs_job_state.stop_job: AttributeError: 'AsynchronousJobState' object has no attribute 'stop_job' It seems that galaxy had received job status from pbs, but pbs.py can't handle message correctly. Is there any solution to solve this problem? Thanks, Peter

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Tool-shed - bowtie and tophat dependency
by Shantanu Pavgi (Campus) 11 Sep '13

11 Sep '13

We have migrated bowtie tool wrapper from dist to tool-shed using migration script # 7 with install_dependencies option. We removed our locally installed bowtie binaries so that install_dependencies option would work fine. I think an earlier release would skip dependency installation if they were found in PATH. The tool-shed installed bowtie is working fine, however, dist included tophat is broken now as it is failing to find bowtie binaries. Should we install back bowtie outside of tool-shed OR is there a tophat wrapper that can handle this dependency? Any pointers? -- Thanks, Shantanu

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Stable Galaxy to install.
by cngbgalaxy＠gmail.com 10 Sep '13

10 Sep '13

Hi everyone, I want to install my local Galaxy,and I don't know which version is more stable and work well.Could anyone give same advise?Thank you very much. cngbgalaxy(a)gmail.com

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Looking for brave testers. New barcode splitter outputing splitted datasets directly to the history.
by Carlos Borroto 10 Sep '13

10 Sep '13

Hi, I was wondering if I could get someone to test this new barcode splitter I wrote. The main reason for me to duplicate the already great fastx-toolkit based splitter, is so I can use galaxy's multiple output capabilities. You can find this tool in the testtoolshed for now(after some more testing I will moved to the main toolshed): http://testtoolshed.g2.bx.psu.edu/view/cjav/split_by_barcode Hopefully I got Galaxy's tool dependency system right(it works on my box, not that this says much) and installing this tool should be quite easy. I have to say big thanks to Biopython and this[1] anonymous soul for making it quite easy to write the actual code doing the heavy lifting. [1]https://gist.github.com/dgrtwo/3725741 Cheers, Carlos

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External Access of user data
by Brauer, Janos 10 Sep '13

10 Sep '13

Hello, I was wondering if there is any possibility to access user data from a galaxy user using plugins such as OmniAuth. Of course the user would first have to permit access for the web service using tools such as OmniAuth. If OAuth is not yet available, it would be a nice feature to add. Best regards, Janos Brauer

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"Select" in "Filter and Sort" fail to work.
by shenwiyn 10 Sep '13

10 Sep '13

Galaxy Tearm, I use "Select" in "Filter and Sort" to sort my sam file in my local Galaxy.But I got "no peek " under "Matching pattern: ^@" ,while I got the same sam file under "NOT Matching pattern: ^@" .Actually,I can got the correct results in Galaxy main,I don't know what happened to my local Galaxy .I use 009088d5e76f as my local Galaxy. my sam file as follow: @HD VN:1.0 SO:coordinate @RG ID:rg1 SM:s1 @RG ID:rg2 SM:s3 @SQ SN:chr1 LN:10001 @SQ SN:chr2 LN:100001 @SQ SN:chr3 LN:10001 @SQ SN:chr4 LN:1001 bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 shenwiy

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Re: [galaxy-dev] Large files in blend4j
by Eric Kuyt 10 Sep '13

10 Sep '13

Hi John, Some news on the debugging yet? I managed to deploy blend4j in my local maven installation, so now I can test the client.setChunkedEncodingSize(CHUNKED_ENCODING_SIZE); line on my setting. Unfortunately with ChunkedEncoding enabled, it seems that the file is not (recognized by || sent to) galaxy. this is the errormessage: galaxy.web.framework ERROR 2013-09-10 16:06:15,688 Uncaught exception in exposed API method: Traceback (most recent call last): File "/opt/galaxy_testing/lib/galaxy/web/framework/__init__.py", line 189, in decorator rval = func( self, trans, *args, **kwargs) TypeError: create() takes exactly 3 arguments (2 given) 10.79.24.114 - - [10/Sep/2013:16:06:15 +0200] "POST /galaxy_testing/api/tools?key=1234567890abcdef1234567890abcdef1 HTTP/1.1" 500 - "-" "Java/1.7.0_25" Do you know this problem, or could there also be something wrong with my config? Thanks for the fast reply! On 9 September 2013 19:51, John Chilton <chilton(a)msi.umn.edu> wrote: > Glad to hear blend4j is working well, annoyed to here it is not > streaming files out by default. > > Based on your ideas I started some work here, but it is not right. I > spent the last half an hour looking around Galaxy trying to figure out > why history creation via the API was broken, not realizing it was > because I called setChunkedEncodingSize on the client. > > https://github.com/jmchilton/blend4j/commit/22608de210f805fc192c86a836ea55c… > > I have created an issue in github for this: > > https://github.com/jmchilton/blend4j/issues/5 > > Feel free to try to hack on this some more, it might actually take > some non-trivial refactoring to get > client.setChunkedEncodingSize(CHUNKED_ENCODING_SIZE); to be set > conditionally somehow. Right now all requests are sharing the same > underlying client object. > > I will try to work on this more as I have time. > > -John > > On Mon, Sep 9, 2013 at 10:58 AM, Eric Kuyt <eric.kuijt(a)wur.nl> wrote: >> Hi all, >> >> I'm using blend4j for some time now and I'm quite happy about it, but >> now I run into some OutOfMemory issues. >> When I try to upload large files to galaxy (I know http might be not >> the best option) some byte array is getting to large. A possible >> solution would be file chunking in jersey, is this possible in blend4j >> and how could I implement this feature? >> >> Thanks, >> >> Eric >> > > -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

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