#!/bin/bash

set -ve

if [ -z ${CTAT_GENOME_LIB} ]; then
    echo "Error, must have CTAT_GENOME_LIB env var set"
    exit 1
fi

VERSION=`cat VERSION.txt`

# run STAR-Fusion
cd ../ && singularity exec -e -B ${CTAT_GENOME_LIB}:/ctat_genome_lib Docker/star-fusion.v${VERSION}.simg  /usr/local/src/STAR-Fusion/STAR-Fusion --left_fq testing/reads_1.fq.gz --right_fq testing/reads_2.fq.gz --genome_lib_dir /ctat_genome_lib -O testing/test_singularity_outdir/StarFusionOut --FusionInspector inspect --examine_coding_effect --denovo_reconstruct

