could you make KMC from the toolshed (available Galaxy Australia) also available in usegalaxy.eu?

usegalaxy.eu support
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could you make KMC from the toolshed (available Galaxy Australia) also available in usegalaxy.eu?

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Hi @bejo

Is this the tool you are asking about? I see it at both servers.

Link at EU → https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.3+galaxy0

Link at AU → https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/5.0.1+galaxy2

You can share the link to the tool at the AU server if you are asking about something different. Load up the tool, and in the upper right corner find the Options menu. There will be a “Copy link” for the tool, then paste that back here. :slight_smile:

Please let us know how this works out or if you need more help!

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Hi Jennaj,
I am looking to forward to use this tool in Galaxy.

I do not find it in the list of “tools”, however it seems it can be used in Galaxy?

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Hi @bejo

Ok, thanks for posting back that repository link, it helps to clarify!

The tool suite seems to be in the ToolShed, which is a start to getting this on the public UseGalaxy servers. → Galaxy | Tool Shed

However, I don’t see the tool at the UseGalaxy.org.au server yet, so this is probably still being worked on. We can try to get feedback from one of the scientists from that server – hi @igor would you know more about this tool suite? Thanks!

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Hi @jennaj , hi @bejo
Currently KMC is available only on our dev server. I was told it can be installed on the production server. At least, we can try: the wrapper was not updated for two years.
Kind regards,
Igor

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Hi Jannaj and Igor,
Sounds good, though I feel it might not work? Anyway, let’s try it I would say.

Kind regards,

Bejo

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Hi Bejo,

yep, you are right. We found a minor bug on the dev server. The wrapper will be fixed and updated. After that we can go ahead with the tool installation.

Kind regards,
Igor

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Hi @igor any news about KMC?

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Hi @bejo ,

Here are the latest news. KMC wrapped was patched and updated in the tool shed. The pull request for installation to Galaxy Australia prod server has been submitted yesterday. It is now with the server admins.
I’ll let you know when the tool will be available on the server.

Kind regards,
Igor

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Hi @igor, great to hear the progress. Looking fwd to start using the tool.

cheers,

Bejo

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Hi @bejo
KMC tools are available at Galaxy Australia now.
Kind regards,
Igor

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Great Igor! Thanks for getting this done! But unfortunately I am an .eu user! :blush: I was not aware I had to indicate this to you!

I will register myself at Australia too, assuming there are no geolocation issue using different galaxy hubs.

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Hi @bejo
Mayby try KMC on Galaxy Australia and check if it works for you. It is OK to have accounts on different public Galaxy servers. You can move data directly between Galaxy servers. If it works for you, contact Galaxy Europe people, for example, Wolfgang Maier (wm75). KMC is available in Galaxy tool shed, and I do not expect any issue with installation to other Galaxy servers. I cannot add tools to Galaxy Europe.
Kind regard,
Igor

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I will try KMC on Galaxy Australia. Keep you posted with the progress

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I created an account on Galaxy Australia and KMC is working fine! Great help from the Galaxy team to make this available :clap: :+1: :+1: :+1:

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@igor KMC seems to run fine. however, it runs into an error using just a fasta file with a gene sequence. Might be due to the length of a gene?
A workaround is to go via Jellyfish, and use the result of the dump function in Jellyfish as input to construct a KMCdb.

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Hi @bejo
Do you mean KMC Counter? If yes, it fails on very small fasta files, in my case, it was a single tiny sequence.
You can report the error on Galaxy Australia and communicate directly with the person who wrapped the tool. It can be minimal data requirement for the tool.

Kind regards,
Igor

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yes the KMC Counter. I had the impression my gene was too long… I will report the error at Galaxy Australia

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@igor What I like about Galaxy is that datasets are analyzed in parallel. However with KMC it seem not working as I expect it should work. Would it be possible, for example, if you have a sequence library with FWD and REV reads to run KMC counter analysis both sets in parallel? So you wont have to start the KMC counter job twice with the same settings?

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Hi @bejo , you could use a workflow to manage how jobs process in a batch.

Now, when working at a public server, the jobs may still run in a series – it depends how many total jobs are scheduled to run at the same time (there are practical concurrency limits) – but a workflow is usually how this is done, and will schedule the work much quicker than manually running tools 1-by-1, maximizing throughput.

If you are not sure how to use a workflow yet, this is my favorite “getting started” tutorial. It shows how to extract a workflow from a history. :slight_smile: Hands-on: Galaxy Basics for everyone / Galaxy Basics for everyone / Introduction to Galaxy Analyses

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