Added bash script and changed the paths for all files to run from Ope…

…nPBTA directory

analyses/molecular-subtyping-EPN/run-molecular-subtyping-EPN.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+
+# Run `00-subsetting-files-for-EPN.py`  to subset gene expression data and 
+# Run `01-make_notebook_RNAandDNA.py` to match RNA and DNA Biospecimen ID's based on corresponding matching  sample_ID from pbta-histologies.tsv  file and 
+# Run `02_ependymoma_generate_all_data.py` to combine data  from various output files for EPN samples that can be used to categorize samples under different EPN subtypes 
+
+set -e 
+set -o pipefail 
+
+
+# This option controls whether on not the step that generates the EPN only
+# files gets run -- it will be turned off in CI
+SUBSET=${OPENPBTA_SUBSET:-1}
+
+if [ "$SUBSET" -gt "0" ]; then
+  echo "Subsettibg  for CI"
+  python3 analyses/molecular-subtyping-EPN/00-subsetting-files-for-EPN.py
+fi
+
+echo "Generating analyses/molecular-subtyping-EPN/results/EPN_molecular_subtype.tsv that maps DNA and RNA ID's"
+python3 analyses/molecular-subtyping-EPN/01-make_notebook_RNAandDNA.py
+
+echo  "Generating analyses/molecular-subtyping-EPN/results/EPN_all_data.tsv  that has all the relevant data needed for subtyping"
+python3 analyses/molecular-subtyping-EPN/02_ependymoma_generate_all_data.py
+