Commit 675abf78 authored by David Hoksza's avatar David Hoksza
Browse files

clinvar

parent 0658937b
#!/usr/bin/env bash
# ------------------------- PARAMETERS TO SET -------------------------
ORPHANET_IDS="130"
#ORPHANET_IDS="130"
ORPHANET_IDS="33,67046,79327,79321,86309"
DISGENET_CNT_THRESHOLD=50
DISGENET_ASSOCIATION_SCORE_THRESHOLD=0
OPENTARGETS_CNT_THRESHOLD=50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD=0
BUILD_MAP_GENERATOR=0 #1 for building it
STOP_AFTER_STAGE=1
STOP_AFTER_STAGE=-1
# ------------------------- PARAMETERS TO SET -------------------------
ASSOCIATIONS_DIR=associations/
......@@ -18,7 +20,6 @@ ENRICHMENT_CONFIG=${ENRICHMENT_DIR}/config.txt
MAP_GENERATOR_DIR=map_generator/
PYTHON_BIN=python3
#ORPHANET_IDS="33,67046,79327,79321,86309"
ORPHANET_IDS_UNDERSCORE=${ORPHANET_IDS//,/_}
mkdir $RES_DIR
......@@ -79,7 +80,7 @@ fi
echo "Map generator built"
echo "Assembling the map from pathways ..."
map_out_path=${RES_DIR}/06-minerva_map-id_${ORPHANET_IDS_UNDERSCORE}.xml
java -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --output-file ${map_out_path}
java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file ${enriched_maps_out_path} --output-file ${map_out_path}
echo "Pathways assembled into ${map_out_path}"
echo "Combining map with overlays"
......
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