Question: Unable to see my data in the job column
0
gravatar for waliamannu
4.0 years ago by
waliamannu0
Australia
waliamannu0 wrote:

I have registered myself first in the begining. I uploaded two txt files to be analysed.

But when i begin for a job , I am unable to see my data sets in the job column.

The data is succesfully uploaded but dont apear in the job column.

galaxy • 888 views
ADD COMMENTlink modified 3.2 years ago by Martin Čech ♦♦ 4.5k • written 4.0 years ago by waliamannu0

With job column you mean the history panel on the right side of your Galaxy workbench? How do you know its successfully uploaded? Usually you see a yellow box in the history panel with a spinning wheel, that box will turn green if the dataset is uploaded.

ADD REPLYlink written 4.0 years ago by Bjoern Gruening5.0k

Dear Bjoern,

The data has been uploaded succesfully as indicated by the green colour. However now if I plan to say join two data sets. the data sets doesnt show up in the tool pull down menu. You need to assign the data for the job right? I do not see any data in there.

ADD REPLYlink written 4.0 years ago by waliamannu0

Dear Jen,

Thanks for the prompt reply. I understand your queries. satifying everything above I still do not see my data sets in input for a tool in the pull-down menu.

 

Thanks

 

Mannu

ADD REPLYlink written 4.0 years ago by waliamannu0

Hi Mannu, Are you on usegalaxy.org? Also, what tool are you using ("Join two Datasets")? This accepts most tabular datatypes, but what are your inputs set as? Sounds like we are close to a solution. -Jen

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Jennifer Hillman Jackson24k

Dear Jen,

I am on https://usegalaxy.org/. In the tools section I am trying to perform Operate on Genomic Intervals. I have two seperate gene lists as excel files which I have converted to tab delimited format and I want to find an overlap between the two. For this I am using join or the intesect function from the tools.

Do you mean I have to make my file format into tabular format?

many thanks for helping me out with this.

best regards

 

Mannu

ADD REPLYlink written 4.0 years ago by waliamannu0
1

Mannu - Lucky guess on Excel :)

Yes, tabular is good for many things, but since you are using the Operate on Genomic Intervals tools (not just Text Manipulation Tools) I would go ahead and assign the datatype as "interval". This is still tabular data, but has specific fields assigned. See the wiki below for the details. And if your start coordinate is not already 0-based, use the tool "Compute" to subtract "1" from your start, then the tool "Cut" to rearrange your data (substituting in the new 0-based start, and dropping the old one). Use the tool panel search to find tools by name.

OK - here's the datatype wiki: https://wiki.galaxyproject.org/Learn/Datatypes#Interval

The first two plus the fourth protocols in the "Using Galaxy" paper might be of interest, too. The first demonstrates a join operation, the second how to convert almost any file to interval (as long as the data is in there, it can be arranged and labeled), and the fourth covers all of the Genomic Interval functions. It can be found here: https://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012

Good luck! jen

ADD REPLYlink written 4.0 years ago by Jennifer Hillman Jackson24k
1
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Bjoern is correct: first make certain that the datasets are loaded.

But, since you are new to Galaxy, I am wondering if you mean that the datasets are not showing up as input for a tool in the pull-down menu? This can occur when the 'datatype' attribute is not set as one that is recognized by the tool. If so, this is easily remedied, as described in the wiki below, by editing the dataset attribute.

The important point is to read the tool's help (directly on the tool form) to note what the expected input type is, then check to be certain your data meets that criteria, and finally to assign the datatype to match. You can do this during upload or anytime after.

https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

For example, an Excel spreadsheet is not acceptable input, but a text file output from that spreadsheet in tabular format, then uploaded and set as datatype "tabular" or "interval" in Galaxy is. (Each tool has a specific expected set of input types).

Hopefully this helps, but if you still need help, send more details about the specific tool you are using and what format your data is in (general) and the current assigned datatype.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson24k
0
gravatar for waliamannu
4.0 years ago by
waliamannu0
Australia
waliamannu0 wrote:

Dear Jen,

All works well. Highly appreciate your help in this regards. Wish you all the best in what you do.

best regards

 

Mannu

ADD COMMENTlink written 4.0 years ago by waliamannu0
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