Step-by-step instructions

Start by opening a Terminal session on your local system

Set some Google Cloud and other environment variables on your local system

The following environment variables are used merely for convenience and should be customized to produce intuitive labeling for your own analysis:

export GCS_PROJECT=jlf-rcrf
export GCS_SERVICE_ACCOUNT=cromwell-server@$GCS_PROJECT.iam.gserviceaccount.com
export GCS_BUCKET_NAME=jlf-rcrf-immuno-outputs
export GCS_BUCKET_PATH=gs://$GCS_BUCKET_NAME
export GCS_CASE_NAME=jlf-100-044
export WORKING_BASE=~/Desktop/rcrf/$GCS_CASE_NAME

Login to GCP and set the desired project on your local system

From the command line, you will need to authenticate your cloud access (using your google cloud account credentials). This generally only needs to be done once, though there is no harm to re-authenticating. The login command below will generate a custom URL to enter in your browser. Once you do this, you will be prompted to log into your Google account. If you have multiple Google accounts (e.g. one for your institution/company and a personal one) be sure to use the correct one. Once you have logged in you will be presented with a long code. Enter this at the prompt generated by the login command below. Finally, set your desired Google Project. This Project should correspond to a Google Billing account in the Google console. If you are using Google Cloud for the first time, both billing and a project should be set up before proceeding. Configuring billing alerts is also probably wise at this point.

gcloud auth login
gcloud config set project $GCS_PROJECT
gcloud config list

Local setup

First create a working directory on your local system

The following directory on the local system will contain the RNA results from the immuno pipeline that will enable you to run the fusion filtering script.

mkdir -p $WORKING_BASE
cd $WORKING_BASE
mkdir final_results
cd final_results

Download relevant output files

This analysis requires files from pVACfuse and rnaseq directories from the final results.

gsutil -m cp -r \
  "gs://jlf-rcrf-immuno-outputs/JLF-100-038-v2/final_results/final_results_BG/pVACfuse" \
  .

mkdir rnaseq
cd rnaseq
gsutil -m rsync -r -x '.*\.(bam|bai)$' gs://jlf-rcrf-immuno-outputs/JLF-100-038-v2/final_results/final_results_BG/rnaseq .

docker run -it --env WORKING_BASE -v $WORKING_BASE/:$WORKING_BASE/ -v /$HOME/.config/gcloud:/root/.config/gcloud kcotto/fusion_review /bin/bash

cd $WORKING_BASE
python3 /opt/scripts/filter_fusions.py -WB  $WORKING_BASE -f final_results