Difference between revisions of "Build a core-genome phylogeny"
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<syntaxhighlight lang="Bash" line='line'> | <syntaxhighlight lang="Bash" line='line'> | ||
| + | # download repo from metagenlab | ||
git clone https://github.com/metagenlab/eutils.git | git clone https://github.com/metagenlab/eutils.git | ||
| + | |||
| + | # move to eutils directory | ||
| + | cd eutils | ||
| + | # add path to pythonpath and path | ||
| + | echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc | ||
| + | echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc | ||
| + | source ~/.bashrc | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 12:06, 24 October 2018
Overview
This tutorial describes step by step the reconstruction of a core genome phylogeny for a given clade of bacteria.
Setup
- clone the necessary repositories
1# download repo from metagenlab
2git clone https://github.com/metagenlab/eutils.git
3
4# move to eutils directory
5cd eutils
6# add path to pythonpath and path
7echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc
8echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc
9source ~/.bashrc
- install miniconda
- create a dedicated environment and install orthofinder
1# create a new environment
2conda create -n orthofinder
3source activate orthofinder
4# install orthofinder
5conda install orthofinder
6# install biopython
7conda install biopython
Get table of genome assemblies
1df -h
Download gbff files
1df -h