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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
97 stars 27 forks source link

Geopts #10

Closed stu2 closed 9 years ago

stu2 commented 9 years ago

Hi, I had to tweak Clusterflow a bit to get it going on our GridEngine clusters. We needed to use env perl instead of perl because our perl is installed as a module. I haven't tested it on anything else but this branch seems to work now. Also added other GE options and fixed bugs. Cheers, Stuart

ewels commented 9 years ago

Hi @stu2,

This looks excellent - thank you for your work on Cluster Flow, looks like you've made some really nice changes here.

One thing before I merge - would you mind editing or resubmitting the pull request to merge into the v0.4devel branch instead of master? It looks like you've forked from that branch anyway (correctly), and I haven't done anything on it since then so it should be easy. I try to keep the master branch clean as of the latest release, plus it will make it easier for me to review the changes as they won't be mixed in with mine :)

It also looks like you've been struggling with the bowtie2 paths. I feel responsible for your pain, apologies for the way that this has been hacked together to date. It's one of the main things that I would like to rewrite for the next release (when I find the time).

Phil