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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

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.