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Phyluce

Phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.

Usage

Phyluce can be activated using the module file:

module load apps/binapps/phyluce/1.5.0

Phyluce makes use of the apps/python/conda module, therefore this module will be loaded by loading Phyluce. As Phyluce is a Python package your default Python interpreter will be changed by loading Phyluce.

Installation notes

As root:

$ module load apps/python/conda
$ conda create -p /usr/local/packages6/apps/binapps/conda/phyluce python=2
$ source activate /usr/local/packages6/apps/binapps/conda/phyluce
$ conda install -c https://conda.binstar.org/faircloth-lab phyluce

This installs Phyluce as a conda environment in the /usr/local/packages6/apps/binapps/conda/phyluce folder, which is then loaded by the module file phyluce/1.5.0, which is a modification of the anaconda module files.