Can't get 'Get organelle from reads' to work

Hi everyone,

Sorry in advance for the dumb question… I am trying to use GetOrganelle to reconstruct a plant plastome (genome skimming data) and I stay stuck with a message telling me that for mandatory ‘Reference data’ there are no options available (see screenshot below).

I imagine that there must be a way to provide reference data (whether custom - and I can provide some - or Genbank plant plastome database) and that the process must be explained somewhere… but I can’t find the info! Could you help with that ?

Thanks for the help and all the best,

Hi @XavierA

The index needs to be provided by the server admins based on the way the tool form was written.

I did find an open ticket where some changes were made by the developer to make the tool friendlier to a Galaxy installation. The issue is still open, please see Make database paths configurable - add GetOrganelle to Galaxy · Issue #64 · Kinggerm/GetOrganelle · GitHub

Ping @bernt-matthias – do you have any more information to share? I’m guessing this is not quite usable yet at the public sites. Any updates appreciated :slight_smile:

For reference, many tools do have an option to supply reference data from the history but this particular tool wrapper was not written that way. The usual function is for a custom genome or other -ome (a fasta file) and the how-to is here Reference Genome FAQs.

Dear @jennaj

Thanks for the rapid answer and update! Ok, so I’ll wait for the implementation of the datasets in Galaxy (thanks for helping with that @bernt-matthias !) and in the meantime will try Get Organelle on other servers!

All the best!

@jennaj the issue is outdated. I closed it.

So the tool should be fully functional. The reference data needs to be added by the server admins, you need to get in contact with them.

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Dear @bernt-matthias

Thanks for your answer! I’m contacting galaxy‧eu and hope that they will soon upload the reference data!


HI all,

Just an update to tell that galaxy has now uploaded the reference data and that it now works :partying_face:
Than you @bjoern.gruening for your great help!

Best wishes,

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