2
$\begingroup$

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.

Improve this question
$\endgroup$
0

2 Answers 2

Reset to default
2
$\begingroup$
  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).

Improve this answer
$\endgroup$
0
$\begingroup$

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.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.