-
Notifications
You must be signed in to change notification settings - Fork 5
/
format_db.sh
executable file
·41 lines (36 loc) · 1.23 KB
/
format_db.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
#!/bin/sh
# Genoogle: Similar DNA Sequences Searching Engine and Tools. (http://genoogle.pih.bio.br)
# Copyright (C) 2008,2009 Felipe Fernandes Albrecht (felipe.albrecht@gmail.com)
#
# For further information check the LICENSE file.
#
# ----------------------------------------------------------------------------------------
# Script to run the data banks format.
#
# Environment Variables:
#
# GENOOGLE_HOME Point at your Genoogle base directory.
#
# JAVA_HOME Must point at your Java Development Kit installation.
# Required to run the with the "debug" or "javac" argument.
#
# ----------------------------------------------------------------------------------------
if [ -n "${GENOOGLE_HOME+x}" ]; then
echo "\$GENOOGLE_HOME=$GENOOGLE_HOME"
else
echo "\$GENOOGLE_HOME is not set. Using `pwd`"
GENOOGLE_HOME=`pwd`
echo "\$GENOOGLE_HOME=$GENOOGLE_HOME"
fi
if [ -d ${GENOOGLE_HOME}/conf ]; then
echo "Configuration files is $GENOOGLE_HOME/conf/conf.xml"
else
echo "Configuration directory not found. Please configure correctly \$GENOOGLE_HOME."
return
fi
$JAVA_HOME/bin/java \
-server \
-Xms1024m \
-Xmx2048m \
-classpath ${GENOOGLE_HOME}/genoogle.jar:${GENOOGLE_HOME}/lib/* \
bio.pih.genoogle.Genoogle -g