Commit 6940442d authored by David Hoksza's avatar David Hoksza
Browse files

assemble update

parent 40671fc5
......@@ -8,8 +8,8 @@ DISGENET_CNT_THRESHOLD=50
DISGENET_ASSOCIATION_SCORE_THRESHOLD=0
OPENTARGETS_CNT_THRESHOLD=50
OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD=0.2
BUILD_MAP_GENERATOR=1 #0 for building it
STOP_AFTER_STAGE=1
BUILD_MAP_GENERATOR=0 #0 for building it
STOP_AFTER_STAGE=-1
# ------------------------- PARAMETERS TO SET -------------------------
ASSOCIATIONS_DIR=associations/
......@@ -71,6 +71,7 @@ mv enriched_disease_maps.txt ${enriched_maps_out_path}
mv enriched_pathways.txt ${enriched_paths_out_path}
echo "Enriched pathways obtained"
if [ ${STOP_AFTER_STAGE} = 2 ]; then
echo "Exiting after stage ${STOP_AFTER_STAGE}"
exit 0
......
......@@ -42,7 +42,7 @@ if( ! ( score >= 0 & score <= 1 )) {
required.packages <- c("biomaRt", "RCurl", "jsonlite", "httr")
new.packages <- required.packages[!(required.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
if(length(new.packages)) install.packages(new.packages, repos='http://cran.us.r-project.org')
library(biomaRt)
......
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