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slimsuite / pafscaff

PAFScaff: Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding.
GNU General Public License v3.0
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Small data example(s) please? #1

Open fubar2 opened 3 years ago

fubar2 commented 3 years ago

There is interest in wrapping this as a tool for any Galaxy server (e.g. https://usegalaxy.org.au/) if you are agreeable?

The person looking at wrapping this knows a little about Galaxy tools but nothing about scaffolding :) so needs to rely on someone who can to provide working toy samples with sensible parameters. A command line sample will show where the toy datasets go and what the default parameters will be - these all into the test.

Users can change them when they run the tool of course.

Please let me know if this is of interest ?

cabbagesofdoom commented 3 years ago

Hi.

Yes, Anna got in touch about this. I'd definitely be interested in helping to get the tool wrapped. One comment, though: whilst PAFScaff can be used for scaffolding, this function is pretty crude compared to more sophisticated reference-based scaffolders like Satsuma2. The primary function of PAFScaff is really about mapping assembly scaffolds onto reference chromosomes.

I can probably generate some yeast toy example data. (It's on the to-do list.) Default parameters are all in square brackets in the list of commandline options, so that's easy enough.

Rich

fubar2 commented 3 years ago

Ok - thanks. I'll let Anna do her due diligence before asking you to do anything. Until then please update this issue if samples that work with command line examples are available? I remain completely ignorant about scaffolding but willing to try running them for you independently.

cabbagesofdoom commented 2 weeks ago

Hi @fubar2. Sorry for never following up on this. It got a bit buried and then years have passed! I am very interested in trying to get this and a few other tools into Galaxy. Is this still something you are involved in?

fubar2 commented 2 weeks ago

Hi @cabbagesofdoom: Yes - I'm still wrapping tools. Demand for this particular one seems to have died down :( Will try to assist if you have any particular packages in mind to wrap for Galaxy?

cabbagesofdoom commented 2 weeks ago

Thanks. I have a whole workflow that I would like to get into Galaxy, which includes this as one of the tools in it. Will you be at ABACBS in a couple of weeks?

fubar2 commented 2 weeks ago

I have a whole workflow that I would like to get into Galaxy, which includes this as one of the tools in it. Will you be at ABACBS in a couple of weeks?

@cabbagesofdoom: I retired 8 years ago so no, not planning to be at ABACBS although living in Sydney.

Getting tools wrapped and distributed through the toolshed is easy enough, and they become available for use in any private Galaxy instance. Planemo is the tool builder's best friend. Some tutorials in the GTN in case you haven't found those yet.

Getting tools installed on the large public usegalaxy servers is more challenging because those have all been carefully reviewed and are curated by the IUC.