brinkmanlab/islandpath repository overview

⁠docker-islandpath

Docker configuration for packaging islandPath-DIMOB into a docker container

First get the code in islandpath repo:

./get_islandpathdimob.sh

Then build the docker container:

docker build -t islandpath .

Run the docker container with the correct path_to_inputouputfolder, input_file and output_file:

docker run -it --rm -v /path/to/inputoutputfolder/:/data islandpath /data/<input_file> /data/<output_file>

To test with the test files, replace only the <path/to/output/folder> with an existing local folder:

docker run -it --rm -v </path/to/output/folder/>:/data islandpath /apps/islandpath/example/NC_003210.gbk /data/NC_003210_gis.txt

Expected results from the test file:

GI_1    351459  374596  
GI_2    496381  520791  
GI_3    1131558 1161675