galaxy-user November 2013

galaxy-user@lists.galaxyproject.org

46 participants
45 discussions

Re: [galaxy-user] galaxy-user Digest, Vol 89, Issue 4
by Cory Dunn 05 Nov '13

05 Nov '13

Dear Graham, Thanks for the info. However, my problem is that the "Tool Version" field is completely empty in my history items (eg. Tophat2, Cuffdiff). I suppose I can check the dependancies list you described, but it would be important to know precisely which version was run on any given query. Best regards, Cory Message: 3 > Date: Tue, 5 Nov 2013 09:45:19 +0000 > From: "graham etherington (TSL)" > <graham.etherington(a)sainsbury-laboratory.ac.uk> > To: Cory Dunn <cdunn(a)ku.edu.tr>, "galaxy-user(a)bx.psu.edu" > <galaxy-user(a)bx.psu.edu> > Subject: Re: [galaxy-user] Cuffdiff version not apparent > Message-ID: > <CE9E6D0A.21768%graham.etherington(a)sainsbury-laboratory.ac.uk> > Content-Type: text/plain; charset="Windows-1252" > > Hi Cory, > A list of Galaxy dependancies can be found on the wiki at: > http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies > ...although many tools allow a range of tool versions. > > You can also identify the information about the specific tool versions by > clicking on the View Details ?i? icon of a history item created by that > tool and looking at the Tool Version field. > If you?re using the Galaxy public server (https://usegalaxy.org/) then > clicking on the ?i? icon of a cuffdiff output file will show: > > Tool Version:cuffdiff v2.1.1 (4046M) > Hope this helps. > > Cheers, > Graham >

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Cuffdiff version not apparent
by Cory Dunn 05 Nov '13

05 Nov '13

Dear Galaxy Staff: I was wondering which version of Cuffdiff is currently running on Galaxy. The wrapper version is 0.0.6, but I did not see the actual version of the underlying software under the "Tool Version" field (please see attached screen grab). Thanks for your help, Cory Dunn [image: Inline image 1]

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Nov 04, 2013 Galaxy Distribution
by Jennifer Jackson 04 Nov '13

04 Nov '13

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Re: [galaxy-user] Galaxy's Tophat 2 -GTF option
by Jennifer Jackson 01 Nov '13

01 Nov '13

Hi Zain, Annotations are used with Tophat2 the same way that they are with Tophat. Open up the full parameters on the tool form and change the option "Use Own Junctions:" to "Yes". Here you can now supply gene models as set related parameters. If actually performing this operation is problematic and producing errors, please submit a bug report, leaving inputs and outputs undeleted, so that we can troubleshoot. The wrapper is still somewhat new. Hopefully this helps & have a nice weekend, Jen Galaxy Team Jennifer Hillman-Jackson http://galaxyproject.org > On Nov 1, 2013, at 3:22 PM, Zain A Alvi <zain.alvi(a)student.shu.edu> wrote: > > Hi Jenn, > > I hope this reaches you well. I was trying to use tophat 2 on the public Pennsylvania Galaxy server and noticed that I was not able to supply the GTF file. Although it lists that providing GTF file is an option on the bottom of the tophat 2. I was wondering if it possible to add the option to provide an GTF file for Galaxy's Tophat 2. I have attached a screen shot for your kind review as well. > > I would really appreciate it if it was possible. > > -G/--GTF [GTF 2.2 file] > Supply TopHat with a list of gene model annotations. > TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will > attempt to align reads to these junctions even if they would not normally be covered by the initial mapping. > > Sincerely. > > > Zain > <Galaxy_Tophat2_GTF.jpg>

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Grouping Histories into related Projects
by Avery DeVries 01 Nov '13

01 Nov '13

Hello, I was wondering if there way any way to group related histories into "Projects" (like a home directory and sub-directories). Currently, I have several annotations/analyses in separate histories related to the same dataset (i.e. one for gene annotation, one for ENCODE elements, etc) and as you can imagine, as I have several other datasets each with separate histories for each analysis I conduct, my Saved Histories page can get pretty convoluted. I would like to keep them in separate histories so I can easily find separate analyses, but I really wish there was a way to group them together so I could parse through my long list of histories quickly. Is this possible to do? Thank you so much Avery *Avery DeVries* africker(a)email.arizona.edu

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galaxy-user November 2013