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I'm working with phage peptides libraries. Currently I'm analysing a massive data set from phage selection, NGS readout, preprocessed already (fasta file). I want to analyse the sequences to cluster peptides according to their consensus motifs. I found that Hammock may be helpful to do this.

Here is the GitHub repo for Hammock: https://github.com/krejciadam/hammock. I downloaded the master, unpacked it, but I don't know how to use it.

I guess I need to compile, but I have no idea what files need to be compiled, how to do it, what software I need use to compile etc.

I work with Mac/terminal.

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  1. Download a release (Hammock_v_1.2.0.7z) from https://github.com/krejciadam/hammock/releases
  2. Unzip
  3. To run the first example:
cd /your_path/Hammock_v_1.2.0/examples/MUSI/
java -jar ../../dist/Hammock.jar full -i musi.fa

As mentioned in the comments, it's in the manual and any further issues need more information (errors etc).

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Answer from @ram-rs, converted from comment:

There's a Hammock.jar file - there' no need to compile Hammock, although they recommend compiling dependencies. Have you tried running java -jar dist/Hammock.jar --help? Follow their steps from Example 1 - it should work.

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