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root/owl/trunk/make-aglappe.sh
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# Line 10 | Line 10
10   tempdir=$1
11   aglappetag=$2
12  
13 < CLASSPATH=.:/project/StruPPi/jars/mysql-connector-java.jar:/project/StruPPi/jars/JRclient-RE817.jar:/project/StruPPi/jars/java-getopt-1.0.13.jar:/project/StruPPi/jars/junit-3.8.1.jar:/project/StruPPi/jars/commons-codec-1.3.jar:/project/StruPPi/jars/xmlrpc-client-3.0.jar:/project/StruPPi/jars/xmlrpc-common-3.0.jar:/project/StruPPi/jars/ws-commons-util-1.0.1.jar:/project/StruPPi/jars/vecmath.jar:/project/StruPPi/jars/Jama-1.0.2.jar:/project/StruPPi/jars/jaligner.jar:/project/StruPPi/jars/jung/collections-generic-4.01.jar:/project/StruPPi/jars/jung/jung-api-2.0-alpha2.jar:/project/StruPPi/jars/jung/jung-graph-impl-2.0-alpha2.jar
13 > # compile with Java5 to keep it backward compatible
14 > JAVAVERSION=1.5.0
15 >
16 > CLASSPATH=.:/project/StruPPi/jars/mysql-connector-java.jar:\
17 > /project/StruPPi/jars/JRclient-RE817.jar:\
18 > /project/StruPPi/jars/java-getopt-1.0.13.jar:\
19 > /project/StruPPi/jars/junit-3.8.1.jar:\
20 > /project/StruPPi/jars/commons-codec-1.3.jar:\
21 > /project/StruPPi/jars/xmlrpc-client-3.1.jar:\
22 > /project/StruPPi/jars/xmlrpc-common-3.1.jar:\
23 > /project/StruPPi/jars/ws-commons-util-1.0.2.jar:\
24 > /project/StruPPi/jars/vecmath.jar:\
25 > /project/StruPPi/jars/Jama-1.0.2.jar:\
26 > /project/StruPPi/jars/jaligner.jar:\
27 > /project/StruPPi/jars/jung/collections-generic-4.01.jar:\
28 > /project/StruPPi/jars/jung/jung-api-2.0-beta1.jar:\
29 > /project/StruPPi/jars/jung/jung-graph-impl-2.0-beta1.jar:\
30 > /project/StruPPi/jars/jung/jung-algorithms-2.0-beta1.jar
31  
32   cd $tempdir
33  
# Line 36 | Line 53
53   # compiling
54   echo "Compiling..."
55   cd $aglappetag
56 < javac proteinstructure/*.java tools/*.java tinker/*.java sadp/*.java
56 > javac *.java proteinstructure/*.java tools/*.java tinker/*.java sadp/*.java sequence/*.java actionTools/*.java ppi/*.java
57  
58   # creating jar file
59   echo "Creating jar file: $aglappetag.jar ..."

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