May 15, 2020

Public workspaceInstallation instructions for phylogenetic analysis using a conda environment V.1

DOI
dx.doi.org/10.17504/protocols.io.bgd4js8w
  • 1Fundação Oswaldo Cruz / Instituto Gonçalo Moniz
Laise Moraes
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DOI: dx.doi.org/10.17504/protocols.io.bgd4js8w
Protocol Citation: Laise Moraes 2020. Installation instructions for phylogenetic analysis using a conda environment. protocols.io https://dx.doi.org/10.17504/protocols.io.bgd4js8w
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: May 14, 2020
Last Modified: May 15, 2020
Protocol Integer ID: 37020
Abstract
The purpose of this protocol is to define and provide instructions for creating a conda environment for phylogenetic analysis
Installing Miniconda
Installing Miniconda
Open a terminal (Ctrl + Alt + T).
Create a directory called softwares to your HOME directory, switch to it and then download the 64-bit Python 3 Miniconda installer.
Install Miniconda quietly, accepting defaults.
After installation, remove the Miniconda installer from directory.
Set the Miniconda permanent PATH and update conda packages to the latest compatible version.

Command
mkdir $HOME/softwares
cd $HOME/softwares
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -bfp $HOME/softwares/conda
rm Miniconda3-latest-Linux-x86_64.sh
export PATH="$HOME/softwares/conda/bin:/usr/local/share/rsi/idl/bin:$PATH"
echo 'export PATH="$HOME/softwares/conda/bin:/usr/local/share/rsi/idl/bin:$PATH"' >> $HOME/.bashrc
conda update -y -n base conda

Creating conda environment
Creating conda environment
Create a YML file to build a phylogenetic analysis environment called phy.
Command
cat > phy.yml <<EOF
name: phy
channels:
  - bioconda
  - anaconda
dependencies:
  - bcftools
  - biopython
  - bwa
  - clustalo
  - fasttree
  - gbmunge
  - iqtree
  - mafft
  - modeltest-ng
  - phyml
  - samtools
EOF

Create the environment from the phy.yml file
Command
conda env create -f phy.yml