Merge pull request #4616 from nsoranzo/fix_scripts

Fix virtualenv activation for some scripts

create_db.sh

@@ -1,5 +1,6 @@
 #!/bin/sh
 
+cd `dirname $0`
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
 if [ -d "$GALAXY_VIRTUAL_ENV" ];
@@ -8,5 +9,4 @@ then
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
-cd `dirname $0`
 python ./scripts/create_db.py $@

extract_dataset_parts.sh

@@ -1,6 +1,14 @@
 #!/bin/sh
 
 cd `dirname $0`
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
+then
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
+fi
+
 for file in $1/split_info*.json
 do
     # echo processing $file

manage_db.sh

@@ -5,6 +5,7 @@
 # sh manage_db.sh downgrade --version=3 <tool_shed if using that webapp - galaxy is the default>
 #######
 
+cd `dirname $0`
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
 if [ -d "$GALAXY_VIRTUAL_ENV" ];
@@ -13,5 +14,4 @@ then
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
-cd `dirname $0`
 python ./scripts/manage_db.py $@

manage_tools.sh

@@ -1,5 +1,6 @@
 #!/bin/sh
 
+cd `dirname $0`
 : ${GALAXY_VIRTUAL_ENV:=.venv}
 
 if [ -d "$GALAXY_VIRTUAL_ENV" ];
@@ -8,5 +9,4 @@ then
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
-cd `dirname $0`
 python ./scripts/manage_tools.py $@