/icgc-data

scripts for working with icgc data portal

Primary LanguagePython

ICGC data analysis procedure

Run Setup Script

bash icgc_s3_score_client_setup.sh

Add your access token

# From icgc-data/score-client/conf/application.properties
accessToken= # add your token here

Mount the files from the manifest as a FUSE filesystem

sudo mkdir /mnt/icgc
sudo chmod 777 /mnt/icgc

score-client mount \ 
    --mount-point /mnt/icgc \
    --manifest $manifest \
    --cache-metadata

Once you mount the files from the manifest they will be organized into a object_id/file_name directory structure. The object_id and file_name are found in the manifest and will allow us to determine the donor ID as well as what type of sample we have (ie tumor/normal)