updated to exclude the two bridge files that do not load correctly

Dockerfile

@@ -2,7 +2,7 @@ FROM openjdk:11-jdk
 
 MAINTAINER BiGCaT
 
-ENV PORT 8080
+#ENV PORT 8080
 
 RUN apt-get update
 RUN apt-get install jq -y
@@ -18,7 +18,8 @@ RUN /setup.sh
 COPY startup.sh /opt/bridgedb/bridgedb/
 RUN chmod +x /opt/bridgedb/bridgedb/startup.sh
 
-EXPOSE 8183 8080
+EXPOSE 8183 
+#8080
 
 ENTRYPOINT /opt/bridgedb/bridgedb/startup.sh -f /opt/bridgedb-databases/gdb.config
 CMD ["-D", "FOREGROUND"]

setup.sh

@@ -46,17 +46,28 @@ cat gene.json.config >> gdb.config
 cat corona.json.config >> gdb.config
 cat other.json.config >> gdb.config
 
+grep -v "Ec_Derby_Ensembl_91.bridge" gdb.config > tmpfile && mv tmpfile gdb.config
+grep -v "Mx_Derby_Ensembl_85.bridge" gdb.config > tmpfile && mv tmpfile gdb.config
+
 jq -r '.mappingFiles | .[] | select(.tested) | select(.tested|.[]|test(.|"WS")) | "\(.file)=\(.downloadURL)"' gene.json >> files.txt
 jq -r '.mappingFiles | .[] | select(.tested) | select(.tested|.[]|test(.|"WS")) | "\(.file)=\(.downloadURL)"' corona.json >> files.txt
 jq -r '.mappingFiles | .[] | select(.tested) | select(.tested|.[]|test(.|"WS")) | "\(.file)=\(.downloadURL)"' other.json >> files.txt
 
+grep -v "Ec_Derby_Ensembl_91.bridge" files.txt > tmpfile && mv tmpfile files.txt
+grep -v "Mx_Derby_Ensembl_85.bridge" files.txt > tmpfile && mv tmpfile files.txt
+
+
 for FILE in $(cat files.txt)
 do
   readarray -d = -t splitFILE<<< "$FILE"
   echo ${splitFILE[0]}
   wget -nc -O ${splitFILE[0]} ${splitFILE[1]}
 done
 
+#Remove files that do not work
+rm Ec_Derby_Ensembl_91.bridge
+rm Mx_Derby_Ensembl_85.bridge
+
 sed -i -e 's/\t/\t\/opt\/bridgedb-databases\//g' gdb.config
 cp gdb.config /opt/bridgedb/bridgedb/