dockerbiotools/faststructure repository overview

⁠fastStructure

fastStructure⁠ is a tool for inferring population structure from large SNP genotype data.

⁠Building the Docker Container

To build the Docker container:

$ docker build -t dockerbiotools/faststructure .

⁠Running fastStructure

You can run the fastStructure scripts like so:

$ sudo docker run --rm --privileged -v /host/path:/data dockerbiotools/faststructure python script.py

Since Docker containers have isolated file systems and changes to those filesystem do not persist between runs, you will need to mount a local directory inside the Docker container. To do so, replace /host/path with a local directory in the above command. Use the path /data in script arguments.

You can run fastStructure on the test data included with fastStructure like so:

$ sudo docker run --rm --privileged -v ~/Data/fastStructure:/data dockerbiotools/faststructure python structure.py -K 3 --input=test/testdata --output=/data/testoutput_simple --full --seed=100