philippmuench / selection_docker

dN/dS calculation based on codeml, fastcodeml and slimcodeml

selection_docker

calculation of global dN/dS based on codeml, pairwise codeml. Inside the docker you can also run fastcodeml with the fast command.

implemented methods

• PAML (codeml)
• slimcodeml
• fastcodeml
• yn00 (should be installed but not inlcluded in codeml_example.sh)

input file specification

see 'tree.phy' and 'codon.phy' for example input format trees have to be unrooted. You may want to use 'unroot.R' for each run a config file have to be provided, see 'codeml.ctl'(for codeml) and 'codeml_pairwise.ctl' (for pairwise codeml)

usage

this script will run dN/dS analysis on codon.phy and the corresponding tree tree.phy and output the dN/dS

run the scripts (build image local)

sudo docker run hello-world # test if docker is installed
git clone https://github.com/hzi-bifo/selection_docker.git #clone
cd selection_docker 
sudo docker build -t selection_docker . # Should be finished after 3-5 minutes with [...] Successfully built ...
sudo docker run -i -v /absolute_path/to/selection_docker/folder:/data -t --entrypoint /bin/bash selection_docker # enter the docker image
cd data/ 
./codeml_example.sh

run the scripts (use image from docker.io)

sudo docker run hello-world # test if docker is installed
git clone https://github.com/hzi-bifo/selection_docker.git #clone
cd selection_docker 
sudo docker run -i -v /absolute_path/to/selection_docker/folder:/data -t --entrypoint /bin/bash philippmuench/selection_docker # enter the docker image
cd data/ 
./codeml_example.sh

output

• dN/dS will be printed to stdout
• detailed output will be written to test.mlc and test_pair.mlc