--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fetch_databases.sh	Thu Dec 19 13:46:43 2019 +0000
@@ -0,0 +1,35 @@
+#!/bin/bash
+#set -euo pipefail
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+echo "protein databases necessary for full clustering analysis"
+echo "are downloaded from bitbucket repository using git"
+echo ""
+cd $DIR
+git clone https://bitbucket.org/petrnovak/re_databases.git 2> $DIR/.fetchdb.log 
+GITEXIT=$?
+if [ $GITEXIT -eq "0" ]
+then
+    echo "databases successfully downloaded"
+    ln -sf $DIR/re_databases/* $DIR/databases/
+fi
+# cat $DIR/.fetchdb.log
+if [ $GITEXIT -eq "128" ]
+then
+    if grep -q -F "Authentication failed" $DIR/.fetchdb.log
+    then
+        echo "get login credential from (neumann at umbr.cas.cz)!"
+    fi
+    if grep -q -F "already exist" $DIR/.fetchdb.log
+    then
+        echo "repository alredy exists, updating..."
+        cd $DIR/re_databases
+        git pull && ln -f -s $DIR/re_databases/* $DIR/databases/ && find . -type f -exec touch {} +
+    fi
+
+fi
+
+
+
+
+
+