run-gistic-openpbta.sh

#!/bin/bash

# Jaclyn Taroni for ALSF CCDL 2020

# Configure environmental variables for MCR
ORIG_LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/mcr/v83/runtime/glnxa64:/opt/mcr/v83/bin/glnxa64:/opt/mcr/v83/sys/os/glnxa64
export XAPPLRESDIR=/opt/mcr/v83/X11/app-defaults

# This script should always run as if it were being called from
# the directory it lives in.
cd "$(dirname "${BASH_SOURCE[0]}")"

# The gzipped SEG file to use and a "nickname" for it
# The FILEPREFIX is appended to the base file name for the
# gunzipped version of the file in scratch
SEGFILE=${SEGFILE:-"../results/pbta-cnv-consensus-gistic-only.seg.gz"}
FILEPREFIX=${FILEPREFIX:-"consensus"}

# An array list file is used if we want to subset the cohort, by default
# we don't want to do that
ARRAYLIST=${ARRAYLIST:-""}

# The results directory relative to where this script lives
# and the folder name that will contain the GISTIC results, respectively
# These will be constructed into a file path that is the basedir argument
# for GISTIC
RESULTSDIR=${RESULTSDIR:-"../results"}
OUTPUTFOLDER=${OUTPUTFOLDER:-"pbta-cnv-consensus-gistic"}

basedir=${RESULTSDIR}/${OUTPUTFOLDER}
mkdir -p $basedir

# It's unclear if GISTIC can handle gzipped files
# So we will gunzip the file specified and put it in
# a "compartmentalized" scratch folder and name the file
# using the FILEPREFIX variable
scratchdir="../../../scratch/uncompressed-seg-for-gistic"
mkdir -p $scratchdir
segfile=${scratchdir}/${FILEPREFIX}_seg_file_for_gistic.seg
gunzip -c $SEGFILE > $segfile

# This is the correct genome build for OpenPBTA
refgenefile=/home/rstudio/gistic_install/refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat

# Run GISTIC! These parameters are from: https://github.com/d3b-center/OpenPBTA-workflows/blob/cb87a2b725d0e41d34a88436492830802c40f7f0/bash/run-gistic.sh#L16
/home/rstudio/gistic_install/gp_gistic2_from_seg \
  -v 30 \
  -b $basedir \
  -alf $ARRAYLIST \
  -seg $segfile \
  -refgene $refgenefile \
  -genegistic 1 \
  -smallmem 1 \
  -broad 1 \
  -twoside 1 \
  -brlen 0.98 \
  -conf 0.90 \
  -armpeel 1 \
  -savegene 1 \
  -gcm extreme \
  -js 2 \
  -rx 0

# compress GISTIC output
cd $RESULTSDIR && zip -r ${OUTPUTFOLDER}.zip $OUTPUTFOLDER

# 'Undo' environmental variables for MCR
export LD_LIBRARY_PATH=$ORIG_LD_LIBRARY_PATH
unset XAPPLRESDIR