hurwitzlab/fizkin

Name: fizkin

Owner: Hurwitz Lab

Description: All-vs-all sequence comparison for WGS

Created: 2014-09-29 21:00:30.0

Updated: 2017-11-30 22:06:40.0

Pushed: 2018-01-16 20:31:54.0

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Size: 565

Language: R

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README

Fizkin

K-mer analysis.

• “scripts/workers” - driver/worker scripts
• “bin” - necessary compiled tools, e.g., “faSplit”

To Run

• Edit “scripts/config.sh”
• Run “script/0*.sh” in order
• Profit

HPC

These scripts expect to run on PBS, but I am also working on versions to submit to SLURM.

Perl

A couple of scripts use Perl, some CPAN modules, and this:

https://github.com/hurwitzlab/perl-lib

On the HPC systems I use, I find it easiest to use “local::lib” to install the Perl modules I need:

http://search.cpan.org/dist/local-lib/

To see what needs to be installed (assuming you have cpanminus installed):

$ perl Makefile.PL
$ cpanm --install-deps .

Authors

• Bonnie Hurwitz bhurwitz@email.arizona.edu
• Ken Youens-Clark kyclark@email.arizona.edu