Pharokka Database

usegalaxy.eu support
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1

Hi,

I am the developer of Pharokka and am trying to use Pharokka v 1.2.1 on the EU server (the adding of this to the toolshed was extremely helpfully handled by Paul Zierep! thanks Paul!)

When I go to run Pharokka, there is no Database available to run - would you be able to add it?

George

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Hi @gbouras13

Do you want to add indexes for this tool form option? built-in pharokka DB

When wrapping the tool, did you also create a Data Manager to create/add indexes (by an admin)? If not, then try contacting who was helping you before (private), or the EU admins at their Lobby chat here (public) https://matrix.to/#/#usegalaxy.eu:matrix.org. Indexes can be server specific, and not all involve a DM, but that is how to start.

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Hello! I am also trying to use pharokka on this server (Galaxy | Europe), but cannot because it requires selecting a database, but there is none to select.

Bumping this thread as it would be extremely helpful to be able to use this tool. Thank you.

4

You might have more luck by asking at their matrix chat. Or, maybe the developer will post back what is happening so far with an update, ping @gbouras13

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Looks like it works now @juliambrosman (someone in the background fixed it so thanks Galaxy support)!

Iā€™m not responsible for the Galaxy installation, but I am happy to help you install it locally in future if you run into troubles.

1 Like
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Hi! Iā€™m trying to use pharroka on https://usegalaxy.ca/ and Iā€™m facing the same issue with the message:
"Please provide a value for this option.
Using built-in pharokka DB * required"

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Hi everyone in the Galaxy community - this has prompted me, but as the developer of pharokka, how do go about updating it on galaxy? v1.3.2 is 2 years old now, and a new improved database as been released since.

1 Like
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Hi @gbouras13 Great news! This would be great to get updated. Reach out at the IDC chat and let them know what you have and they can help to get this going. See ā†’ https://matrix.to/#/#galaxyproject_idc:gitter.im

Thank you!! :star_struck:

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@gbouras13 the first step is to update the Bioconda package and the Biocontainers.

This has been done: Pharokka | Anaconda.org & Quay

Next step is to update the Galaxy tool tools-iuc/tools/pharokka at main Ā· galaxyproject/tools-iuc Ā· GitHub ā€¦ I can start this update. It would be super helpful if you can tell us which ā€œparametersā€ are new and should be exposed to the user.

Thanks,
Bjoern

ping @paulzierep

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A start is here, but we need a new test database I think: update pharokka to latest version by bgruening Ā· Pull Request #6651 Ā· galaxyproject/tools-iuc Ā· GitHub

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Appreciate it @bjoern.gruening - Iā€™ll reply with more details in the PR on github.

Thanks,
George