Difference between revisions of "Build a core-genome phylogeny"
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# clone [https://github.com/metagenlab/eutils.git eutils] repository | # clone [https://github.com/metagenlab/eutils.git eutils] repository | ||
| − | <syntaxhighlight lang="Bash" line='line'> | + | <syntaxhighlight lang="Bash" line='line'> |
| − | # download repo from metagenlab | + | # download repo from metagenlab |
| − | git clone https://github.com/metagenlab/eutils.git | + | git clone https://github.com/metagenlab/eutils.git |
| − | # move to eutils directory | + | # move to eutils directory |
| − | cd eutils | + | cd eutils |
| − | # add path to pythonpath and path | + | # add path to pythonpath and path |
| − | echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc | + | echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc |
| − | echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc | + | echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc |
| − | # reload bashrc | + | # reload bashrc |
| − | source ~/.bashrc | + | source ~/.bashrc |
| − | </syntaxhighlight> | + | </syntaxhighlight> |
# install [https://conda.io/miniconda.html miniconda] | # install [https://conda.io/miniconda.html miniconda] | ||
Revision as of 12:13, 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 eutils repository
1 # download repo from metagenlab
2 git clone https://github.com/metagenlab/eutils.git
3 # move to eutils directory
4 cd eutils
5 # add path to pythonpath and path
6 echo "export PATH=:$PWD"':$PATH' >> ~/.bashrc
7 echo "export PYTHONPATH=:$PWD"':$PYTHONPATH' >> ~/.bashrc
8 # reload bashrc
9 source ~/.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