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.
> Date: Tue, 5 Nov 2013 09:45:19 +0000
> From: "graham etherington (TSL)"
> To: Cory Dunn <cdunn(a)ku.edu.tr>, "galaxy-user(a)bx.psu.edu"
> Subject: Re: [galaxy-user] Cuffdiff version not apparent
> Content-Type: text/plain; charset="Windows-1252"
> Hi Cory,
> A list of Galaxy dependancies can be found on the wiki at:
> ...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.
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
Thanks for your help,
[image: Inline image 1]
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,
> 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.
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