Updating tools/hictk from version 2.0.2 to 2.2.0

[gxydevbot]

Hello! This is an automated update of the following tool: tools/hictk. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

I have updated tools/hictk from version 2.0.2 to 2.1.1.

Project home page: https://github.com/paulsengroup/hictk/releases

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[SaimMomin12]

We do not have juicebox_hic as a datatype in Galaxy. @bgruening how do we proceed with this?

[bgruening]

mh, damn. Is it this one? https://github.com/usegalaxy-eu/galaxy/blob/release_24.2_europe/lib/galaxy/config/sample/datatypes_conf.xml.sample#L532

[SaimMomin12]

mh, damn. Is it this one? https://github.com/usegalaxy-eu/galaxy/blob/release_24.2_europe/lib/galaxy/config/sample/datatypes_conf.xml.sample#L532

No, it dont think so this is the one. juicebox_hic is some new datatype for hic imho

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[robomics]

I can confirm that juicebox_hic and juicer_medium_tabix.gz are differnt formats.
.hic is a specialized file format used to store interactions from Hi-C and similar experiments.
juicer_medium_tabix.gz as far as I understand is one of the text files accepted by juicer_tools when ingesting pairwise interactions into .hic files.

The quickest way to check if a file is (or rather claims to be) in .hic format, is to read the first 4 bytes, and check if they are equal to HIC\0.

See e.g., the specs for .hic v9.
All format revisions use the same magic string.

hictk has a validate subcommand that can do this (and a few other checks) for you:

hictk validate test/data/hic/ENCFF993FGR.2500000.hic
[2025-06-23 15:28:26.813] [info]: Running hictk v2.1.4
{
    "format": "hic",
    "is_valid_hic": true,
    "uri": "test/data/hic/ENCFF993FGR.2500000.hic"
}
### SUCCESS: "test/data/hic/ENCFF993FGR.2500000.hic" is a valid .hic file.

You can parse the JSON printed to stdout, or just look at the exit code.

Let me know if I can help with adding support for this datatype to Galaxy.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.