Question: fetch genome all fasta tool not found in tool shed
0
gravatar for mohammedtleis
6 months ago by
mohammedtleis0 wrote:

Greetings,

I am looking for the fetch-genome-all-fasta tool to install it on local instance of galaxy; I want to use it to fetch a human genome to be used as a reference genome. But I couldn't happen to find this tool when I search in the toolshed.

I could find it online though and cloned it into a local folder but I have no clue how to include it into Galaxy.

Any suggestions?

Best Regards, M. Tleis

ADD COMMENTlink modified 5 months ago • written 6 months ago by mohammedtleis0

Thanks!

I am still issues using the 'fetch_genome_dbkeys_all_fasta'. After installing , I click on 'Manage Installed Tools' and Click on the button to create a new DBKey or reference genome, But Galaxy got an internal error and a message is supposedly sent to Galaxy team. Now what?

Best Regards, M. Tleis

ADD REPLYlink modified 5 months ago • written 5 months ago by mohammedtleis0

Use the tool under the Admin > Server > Local data. It will not appear in the regular Tool panel. The tutorial here shows how: https://galaxyproject.org/admin/#data-resources

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson24k

Dear Jen,

I am still getting internal server error: Snapshot

Best Regards, M. Tleis

ADD REPLYlink written 5 months ago by mohammedtleis0

Hi - it looks like you changed your prior comment. It is best to post again if you have a new question or change your question.

Your server might be busy. Have you upgraded the database or are you still using the default SQLite?

Do other tools work? Or do you have a screenshot of the settings used with the DM tool? And of the expanded dataset, if loading a fasta from the history? There could be a mix-up in usage there triggering an error.

This tool installed in a brand new v17.09 Galaxy and fetched the sacCer3 from UCSC without any problems. So, I don't think the tool itself is a problem, but rather a load or config issue.

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson24k
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Use this DM: data_manager_fetch_genome_dbkeys_all_fasta

The other one was combined with the above and all functionality was preserved.

  • If the dbkey already exists, that can be specified on the tool form.
  • If it doesn't already exist, a new one can be created on the tool form and will be added to your list of reference genomes in the upload tool and edit attributes form.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson24k
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