lexmapr-docker

Docker container for running LexMapr

Usage

• The LexMapping can be run from the docker cotainer using a single line, providing the files are named input.csv and config.json.

• Move these two files into a directory on the localhost which can be mounted to the docker container.

• The container and lexmapr command are then executed together using;

docker run --name lexmapr -v <LOCAL_DIR>:/data wilsontom/lexmapr-docker

• This is will create an output.tsv file in the <LOCAL_DIR>

cat <LOCAL_DIR>/output.tsv

Sample_Id       Sample_Desc     Cleaned_Sample  Matched_Components
small_simple1   Chicken Breast  chicken breast  ['breast:uberon_0000310']
small_simple2   Baked Potato    baked potato    ['potato (whole, baked):foodon_03302196']
small_simple3   Canned Corn     canned corn     ['corn (canned):foodon_03302665']
small_simple4   Frozen Yogurt   frozen yogurt   ['frozen:pato_0001985']
small_simple5   Apple Pie       apple pie       ['apple pie:foodon_00002475']

Currently the options for running lexmapr are

-p ifsac --no-cache

These settings cab be easily changed by editing the entrypoint.sh script.