Question: Galaxy workflow inputs
0
gravatar for jannetta.steyn
23 months ago by
jannetta.steyn10 wrote:

I guess this is a stupid question because I couldn't find anybody else asking the question and it is very basic. I am trying to use Galaxy to create a workflow.  I have only added one program which is bwa-mem. When I run the workflow I get the page where I am supposed to select the input files, but my data files aren't listed there. I followed the Galaxy101 tutorial and the files were available for selection in the dropdown boxes, but when I try the same thing using bwa-mem or even Tophat my data files are not listed. The dropboxes are emtpy.

I have uploaded fastq files and they are displayed in the history to the right of the screen.

What am I doing wrong?

 

Thanks for any help.

Regards

Jannetta

galaxy • 653 views
ADD COMMENTlink modified 22 months ago • written 23 months ago by jannetta.steyn10
0
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Input datasets need to be added into the workflow. These can be found in the workflow editor at the bottom of the far left tool panel and added to a workflow the same as a tool.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 23 months ago by Jennifer Hillman Jackson23k
0
gravatar for jannetta.steyn
23 months ago by
jannetta.steyn10 wrote:

Hi Jen

Thanks for your comment. I am looking at the bottom of the far left tool panel but I don't see anything resembling inputs. I only see some menu items such as Multiple regression, Multivariate Analysis, Motif Tools, STR-FM and then some deprecated stuff. I don't know what I'm supposed to be looking for. I tried Inputs at the top but that didn't work either.

 

Regards

Jannetta

ADD COMMENTlink modified 23 months ago • written 23 months ago by jannetta.steyn10
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gravatar for jannetta.steyn
23 months ago by
jannetta.steyn10 wrote:

I'm still having no luck finding a way of getting the data files in the selected history into the workflow. Can someone perhaps point me in the right way. I'm going through the videos but so far no luck and these videos take forever to go through especially that what they are about are irrelivant to me when all I want to know is how to select my input files in the workflow.

I must be completely missing something here because I can't even select inputs if I try to run something like bwa-mem just from the menu. I selecte bwa-mem from the tools on the left and then the options are displayed in the middle section of the screen with my selected history to the right. I select the genome and I select paired. The input dropdown boxes for selecting the reads are still empty.

ADD COMMENTlink modified 23 months ago • written 23 months ago by jannetta.steyn10
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gravatar for jannetta.steyn
22 months ago by
jannetta.steyn10 wrote:

I shall answer my own question. I found something remotely related when I googled the problem which put me on the right track.

As far as I'm concerned this is a somewhat ridiculous state of affairs, because I don't understand the need for this feature and I also don't understand why it is not documented in an obvious place.

When you upload a fasta file into a Galaxy history, you wil probably go to "Get Data" on the left hand menu and then "Upload File". When this file eventually appears in the history you can click on the little pencil icon to display its "attributes". In the "work area" of the Galaxy screen, that would be the middle section, the attributes of your files is displayed. However, "Attributes" is only one tab of the work area at this stage. There are also "Convert Format", "Datatype" and "Permissions". If one clicks on "Datatype", there is a heading, "New Type".

So since a fasta file was uploaded, the drop-down box displayes "fasta". Well, in my case it did. I won't be surprised if, for someone else, it displays something totally irrelivant. For bwa-mem this has to be changed to "fastqsanger". Why, I don't know? Until now I have never heard of a "fastqsanger" format file and having used bwa-mem regularly before on a cluster I have never come across this "type". But, since that is what Galaxy insists on, that is what you have to do. Something is then done to the file (what I don't know) because it does go off on a tangent for a while, the background of the file in the History becomes yellow, and then it is made available, when the background goes green again, and the file is available as an input in the dropbox to the bwa-mem tool.

I hope this helps someone else that is as stupid as me.

ADD COMMENTlink written 22 months ago by jannetta.steyn10
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