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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Cool to hic #1382

Closed fubar2 closed 5 months ago

fubar2 commented 5 months ago

Will this do for a start @bgruening Sorry it took so long - I was testing a bad cool file. Once I found a valid one, it worked fine. uses hictk needs logic to consider case of mcool hictk cl expects things to have informative extensions. must take a look at the python bindings - probably more convenient.. Output works with JBrowse2

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fubar2 commented 5 months ago

Yay - the matrix.mcool and cool samples in lib/datatypes/test convert to hic without hictk complaining. Not viewed as don't know the genome but at least it seems to work. Need a scool file to try...

fubar2 commented 5 months ago

You will also need a hic binary:Binary subclass datatype added to datatypes_conf.xml

fubar2 commented 5 months ago

Got a version of jbrowse2 that accepts hicexplorer cool files - here's one from following the GTN tutorial. Note the name of the track file - a cool output from the matrix builder. New conda container to add hictk so let me know when suits for manual update but will be very cool

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bgruening commented 5 months ago

I need to add a datatype before, otherwise I would merge it already.

bgruening commented 5 months ago

We call it juicebox_hic thanks @lldelisle for the suggestion. https://github.com/aidenlab/Juicebox/blob/master/HiCFormatV8.md