Difference between revisions of "Stacks"
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Should you need Stacks to run with the intel compiler you would have to change the environment to ''hpc-env/6.4'' and load Stack with the '' | Should you need Stacks to run with the intel compiler you would have to change the environment to ''hpc-env/6.4'' and load Stack with the ''intel toolchain'': | ||
ml hpc-env/6.4 | ml hpc-env/6.4 | ||
ml Stacks/2.1-intel-2018a | ml Stacks/2.1-intel-2018a | ||
Revision as of 14:00, 17 October 2019
Introduction
Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Installed version
These versions are installed and and currently available ...
... on envirnoment hpc-uniol-env:
Stacks/1.42 Stacks/2.1-foss-2016b
... on environment hpc-env/6.4:
Stacks/2.1-intel-2018a Stacks/2.4-intel-2018a Stacks/2.41-foss-2017b
Using Stacks on the HPC cluster
If you want to use Stacks on the HPC cluster, you will have to load the corresponding module. If you are using the standard environment hpc-uniol-env you can do that by using the command
module load Stacks/2.1-foss-2016b
Should you need Stacks to run with the intel compiler you would have to change the environment to hpc-env/6.4 and load Stack with the intel toolchain:
ml hpc-env/6.4 ml Stacks/2.1-intel-2018a
Documentation
A manual for Stacks can be found here.
