configure to normal settings

Dockerfile

@@ -14,7 +14,7 @@ RUN /setup.sh
 
 #The following 2 lines are normally commented out. For local, small scale testing, they can be used (see setup.sh for explanations). This would require the COPY of the .bridge file, and commenting out all lines related to the automated creation of gbd.config in the setup.sh script.
 #COPY Hs_Derby_Ensembl_108.bridge /opt/bridgedb-databases/
-COPY gdb.config /opt/bridgedb/bridgedb/
+#COPY gdb.config /opt/bridgedb/bridgedb/
 
 COPY startup.sh /opt/bridgedb/bridgedb/
 RUN chmod +x /opt/bridgedb/bridgedb/startup.sh

setup.sh

@@ -23,7 +23,7 @@ cd /opt/bridgedb-databases/
 #BRIDGEDB DATABASES
 #Option 1A: Get bridgedb databases MANUALLY + new download. 
 #If .bridge files are not yet downloaded: For each one, also add line in gdb.config. The Dockerfile should also include the line that copies the gdb.config file.
-wget https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge
+#wget https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge
 #COPY gdb.config /opt/bridgedb/bridgedb/
 
 #Option 1B: Get bridgedb databases MANUALLY without new download.
@@ -34,31 +34,31 @@ wget https://zenodo.org/record/7781913/files/Hs_Derby_Ensembl_108.bridge
 #Option 2: Get all bridgedb databases AUTOMATICALLY. 
 #Comment out all lines below if testing locally on small scale, with a direct COPY of the .bridge file
 
-#wget -nc https://bridgedb.github.io/data/gene.json
-#wget -nc https://bridgedb.github.io/data/corona.json
-#wget -nc https://bridgedb.github.io/data/other.json
+wget -nc https://bridgedb.github.io/data/gene.json
+wget -nc https://bridgedb.github.io/data/corona.json
+wget -nc https://bridgedb.github.io/data/other.json
 
-#wget -nc https://bridgedb.github.io/data/gene.json.config
-#wget -nc https://bridgedb.github.io/data/corona.json.config
-#wget -nc https://bridgedb.github.io/data/other.json.config
+wget -nc https://bridgedb.github.io/data/gene.json.config
+wget -nc https://bridgedb.github.io/data/corona.json.config
+wget -nc https://bridgedb.github.io/data/other.json.config
 
-#cat gene.json.config >> gdb.config
-#cat corona.json.config >> gdb.config
-#cat other.json.config >> gdb.config
+cat gene.json.config >> gdb.config
+cat corona.json.config >> gdb.config
+cat other.json.config >> 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
+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
 
-#for FILE in $(cat files.txt)
-#do
-#  readarray -d = -t splitFILE<<< "$FILE"
-#  echo ${splitFILE[0]}
-#  wget -nc -O ${splitFILE[0]} ${splitFILE[1]}
-#done
+for FILE in $(cat files.txt)
+do
+  readarray -d = -t splitFILE<<< "$FILE"
+  echo ${splitFILE[0]}
+  wget -nc -O ${splitFILE[0]} ${splitFILE[1]}
+done
 
-#sed -i -e 's/\t/\t\/opt\/bridgedb-databases\//g' gdb.config
-#cp gdb.config /opt/bridgedb/bridgedb/
+sed -i -e 's/\t/\t\/opt\/bridgedb-databases\//g' gdb.config
+cp gdb.config /opt/bridgedb/bridgedb/