Question: How to download prokka output in workflow
0
gravatar for opeyemi
9 months ago by
opeyemi0
opeyemi0 wrote:

Hello everyone, Is it possible to download the output of the workflow all at once? I am annotating about 200 bacterial genomes using prokka in workflow. Of course, I got several output formats for each genome and wondering if there is a way the outputs can be downloaded all at once.

Thank you in anticipation for your opinions.

Opeyemi

ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by opeyemi0
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The entire history containing the workflow results can be downloaded. Use the History menu option "Export History to File". Exports take a while to build into a tar archive (size dependent). Click on the given link for status updates to know when it is ready.

To know when the history is ready to download, the last job of a workflow could be set to send an email when completed.

I am not sure if you are using Data collections or not, but data in Collections is not output to history archives yet. This is a priority development area. For now, Collections must be downloaded individually. A potential complication is that collection download is problematic right now at Galaxy Main https://usegalaxy.org. This is likely be resolved quickly. Follow here for updates: https://github.com/galaxyproject/usegalaxy-playbook/issues/85

The final option is to wrap all of this up into a script. If that interests you, help for the Galaxy API and BioBlend are here: - https://galaxyproject.org/develop/api/ - https://bioblend.readthedocs.io/en/latest/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k
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