[galaxy-user] error running cufflinks

2013-02-01 Thread Davide Degli Esposti
Dear Jen, after a couple of days of running cufflinks on a sam file (data 9) with an annotated reference in gtf (data 28), I have this message in return that I am not able to decode: 32: Cufflinks on data 9 and data 28: total map mass error An error occurred running this job:cufflinks v2.0.2

Re: [galaxy-user] Error / Nebula and RepeatMasker

2013-02-01 Thread Sarah Maman
Thanks Bjoern, In your xml file, I 've specified the interpreter : command replace by command interpreter=bash but the problem is not solved (; is supported by our cluster) because the command is runned with an error ;; (double ;) instead of ; (simple ;) : `bash /my/path/to/RepeatMasker

[galaxy-user] gather results from multiple histories

2013-02-01 Thread mark.rose
Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This

[galaxy-user] gather results from multiple histories

2013-02-01 Thread mark.rose
Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This

Re: [galaxy-user] gather results from multiple histories

2013-02-01 Thread Dannon Baker
Hey Mark, Yep, sure can. Just click on the gear in the history panel and go to Copy Datasets, and copy those datasets you're interested in to th specific new history you want to use. -Dannon On Feb 1, 2013, at 10:15 AM, mark.r...@syngenta.com wrote: Hi All Let’s say that I have results

[galaxy-user] error message running Cufflinks on local galaxy

2013-02-01 Thread Davide Degli Esposti
Dear Jen, I have downloaded Galaxy on my computer. When trying to run cufflinks locally I have this error message: 8: Cufflinks on data 3 and data 2: gene expression error An error occurred running this job:Could not determine Cufflinks version cufflinks -q --no-update-check -I 30 -F

Re: [galaxy-user] error message running Cufflinks on local galaxy

2013-02-01 Thread Jennifer Jackson
Hi Davide, Is this the same job as you can on the public Galaxy Main instance (same inputs/settings)? If so, let's review that one once the bug report comes in and see if the there is a data issue we can trace back to as one of the first steps (GTF file or other). Jeremy might also have more

Re: [galaxy-user] error running cufflinks

2013-02-01 Thread Jennifer Jackson
Hi Davide, Would you be able to send this in as a bug report? This will allow us to check out the details. You basically just click on the green bug icon for one of the datasets in the group and submit, but this wiki also explains: http://wiki.galaxyproject.org/Support#Reporting_tool_errors

[galaxy-user] February 2013 Galaxy Update

2013-02-01 Thread Dave Clements
Hello all, The February 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02 at http://wiki.galaxyproject.org/GalaxyUpdates/2013_02 *Highlights:* - Three new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_02#New_Papers -

[galaxy-user] Error using trackster

2013-02-01 Thread Kilaru, Varun
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain

[galaxy-user] Error using Trackster

2013-02-01 Thread Kilaru, Varun
Hi, Good day. I have been trying to use trackster on a file I downloaded from the NCBI GEO. However, it fails with the following error: hashMustFindVal: 'chr11' not found grep: writing output: Broken pipe This is followed by a number of lines of the same error code. I am not sure what is

Re: [galaxy-user] Error using Trackster

2013-02-01 Thread James Taylor
What is the type of the file from GEO? Any additional information you provide will help debug this. -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 1, 2013 at 1:53 PM, Kilaru, Varun vkil...@emory.edu wrote: Hi, Good day. I have been trying to use trackster on a

Re: [galaxy-user] Error using Trackster

2013-02-01 Thread Kilaru, Varun
Hi Professor James Taylor, Good day. Its a .wig file I downloaded from GEO. I tried to upload the zipped version to a previous mail but it is pending moderator approval. I downloaded the file from this link: http://www.ncbi.nlm.nih.gov/epigenomics/19516/ and did not make any changes to the

Re: [galaxy-user] Error using Trackster

2013-02-01 Thread James Taylor
Okay. In Galaxy, what genome build (dbkey) is selected for the dataset? -- James Taylor, Assistant Professor, Biology/CS, Emory University On Fri, Feb 1, 2013 at 3:09 PM, Kilaru, Varun vkil...@emory.edu wrote: Hi Professor James Taylor, Good day. Its a .wig file I downloaded from GEO. I

Re: [galaxy-user] Error using Trackster

2013-02-01 Thread Kilaru, Varun
Hi Professor James Taylor, Good day. This issue is resolved thanks to your foresight. I forgot to give a dbkey to this one dataset and hence it failed to open. Everything is working fine now. Thanks so much once again, Varun From: ja...@taylorlab.org

Re: [galaxy-user] can't download big files

2013-02-01 Thread Allan Sun
Thank you so much for your useful message,Jennifer.The problem is gone after upgrading python from 2.5 to 2.7. Allan Hi Allan, It should be possible to just use the save function (disc icon) to download datasets of this size to your local computer. As for curl, this also is an alternative.

Re: [galaxy-user] Fwd: Converting files to gd_snp format

2013-02-01 Thread Cathy Riemer
Hello Mike, The tutorial you were looking at was made using one of our local Galaxy instances, in advance of updating the main public server. The main server already includes most of the tools used in the examples, but two of the format conversion tools (MasterVar to gd_snp and pgSnp to gd_snp)