problems with drop down menu

Question: problems with drop down menu

3.8 years ago by

United Kingdom

Hi everyone,

Has anyone problems with drop down menu when using Galaxy? I thought it was a problem of Odose, but I noticed it was the same for other tools of Galaxy. Can anyone help me?

Thank you,

Cheers,

Nadia

odose galaxy • 888 views

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modified 3.8 years ago by dr.michielvos • 0 • written 3.8 years ago by nadiaandrea.andreani • 0

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Nadia,

Could you explain which menu is a problem at http://usegalaxy.org? And how it is behaving for you? Including what OS/Browser you are using may help.

Thanks, Jen, Galay team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.8 years ago by

nadiaandrea.andreani • 0

United Kingdom

nadiaandrea.andreani • 0 wrote:

Hi Jen,

I have problems when trying to upload new genome on odose. genome coding region is required but there is no possility to choose any option. it is the same if I try others tools of galaxy: for example the one to convert fastq to fasta. I cannot choose the file!

my OS is windows and I tryed with Chrome, Firefox and Internet Explorer.

Thank you very much!

Nadia

ADD COMMENT • link written 3.8 years ago by nadiaandrea.andreani • 0

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For the issues at the other public Galaxy site, you will need to contact the group that hosts that instance.
http://wiki.galaxyproject.org/PublicGalaxyServers#ODoSE

When using any Galaxy, tools often only recognize datasets that have a compatible "datatype" assigned. For fastq data, this is generally "fastqsanger". Make certain the the quality scores are scaled correctly for this type before just assigning it. More help is in our wiki here, see this section and the those below it:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

Best, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

3.8 years ago by

nadiaandrea.andreani • 0

United Kingdom

nadiaandrea.andreani • 0 wrote:

Thank you Jennifer,

I actually don't think is a problem of odose, but of Galaxy. Furthermore, it is not a problem of the dataset format! the Fastq to fasta was only an example! Once I try one of the tools, the dropdown menu is empty, I cannot choose any option, nor write directly something.

Hope that someone can help me!

Best regards,

Nadia

ADD COMMENT • link written 3.8 years ago by nadiaandrea.andreani • 0

3.8 years ago by

dr.michielvos • 0

United Kingdom

dr.michielvos • 0 wrote:

Hi Jennifer,

Nadia's supervisor here. Just to be more clear I have provided a link to screenshots of the odose upload dialog box that is not working (on the left, circled) and the galaxy upload dialog box (on the right) that now looks different from a few days ago. So I am guessing odose missed a Galaxy update?

https://coastalpathogens.wordpress.com/test/

Any pointers woudl be greatly appreciated!

cheers Michiel

ADD COMMENT • link written 3.8 years ago by dr.michielvos • 0

Hi Michiel,

I do not recognize the upload tool on the left as one that is part of the core distribution or that has been hosted out of the public Tool Shed (http://usegalaxy.org/toolshed). Perhaps it was developed in-house? I would contact the administrator of the ODoSE server and see if they can help more.

The upload tool hosted on the public Main Galaxy site is reviewed here, for comparison: http://wiki.galaxyproject.org/Support#Loading_data

For the tool on the right, that is not an upload tool. That is a dataset conversion tool. It is a new design and can be obtained from the Tool Shed here: https://toolshed.g2.bx.psu.edu/view/devteam/fastq_to_fasta

However, a problem with the Fastq-fasta conversion tool will not be related to an upload issue directly (it does not upload data). Rather, dataset format issues are the most common and seem to be the case here. Note the message in the pull down menu -> there are no datasets with the datatype "fastqsanger" assigned in the active history. This is required input for the tool. See my original comments above for how to assign datatype as needed (including fastq types and reformatting).

Take care, Jen, Galaxy team

ADD REPLY • link modified 3.8 years ago • written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

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