phyluce v1.7.3

phyluce is available in several forms. See documentation for additional details. The preferred installation uses conda. phyluce is also available as a Docker container. Both options include all of the dependencies required by phyluce (which are numerous).

Installation

Conda

1. Install Miniconda by following these instructions
2. Then, for your operating system:

• MacOS - M-Series CPU

  wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-macOS-conda.yml
  
  # the next line must be run at the same time (e.g. do not split it up) - this sets up an x86 environment
  CONDA_SUBDIR=osx-64 conda create -n phyluce-1.7.3-x86 python=3.6
  conda activate phyluce-1.7.3-x86
  conda config --env --set subdir osx-64
  # finally, install from the yml file
  conda env update --name phyluce-1.7.3-x86 --file phyluce-1.7.3-py36-macOS-conda.yml --prune
  # if you are finished
  conda deactivate

• MacOS - Intel CPU

  wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-macOS-conda.yml
  conda env create -n phyluce-1.7.3 --file phyluce-1.7.3-py36-macOS-conda.yml

• Linux

  wget https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.3/distrib/phyluce-1.7.3-py36-Linux-conda.yml
  conda env create -n phyluce-1.7.3 --file phyluce-1.7.3-py36-Linux-conda.yml

4. Activate and use the environment:

conda activate phyluce-1.7.3 # or phyluce-1.7.3-x86 if using M-series CPU

Docker

1. Pull the image from Docker Hub:

docker pull fairclothlab/phyluce:1.7.3

2. See documentation for more specific details, but generally:

docker run fairclothlab/phyluce:1.7.3 <name_of_phyluce_program>

Changes

Bug Fixes

• fixed an issue concatenating phylip files (closes #307)
• updated a failing test (that resulted from changes in the BOLD database)