owl-1.9.3/scripts/make-owl.sh

#!/bin/sh
if [ -z "$2" ]
then
    echo "Usage: make-owl.sh <svn url> <tempdir> [<rev>]"
    echo "e.g. for svn url: svn://black/aglappe/trunk or svn://bioinformatics.org/svnroot/owl/tags/owl-1.2.0"
    echo "Optionally specify a revision to be exported instead of head"
    exit
fi

svnurl=$1
tempdir=$2
rev=""
if [ -n "$3" ]
then
        rev=$3
fi

echo "Compiling with:"
javac -version
echo ""


cd $tempdir

tag=`basename $svnurl` 

revStr=""
if [ -n "$rev" ]
then 
        revStr="-r $rev"
fi

# exporting from svn
echo "Exporting source from svn"
svn export $revStr $svnurl
if [ "$?" -ne "0" ]
then
        echo "Couldn't export from svn. Exiting"
        exit 1
fi


# compiling
echo "Compiling..."
cd $tag/src


jarfiles=`ls ../jars/*.jar`
CLASSPATH="."
for jarfile in $jarfiles
do
        CLASSPATH="$jarfile:$CLASSPATH"
done
jarfiles=`ls ../jars/uniprot/*.jar`
for jarfile in $jarfiles
do
        CLASSPATH="$jarfile:$CLASSPATH"
done

echo $CLASSPATH


javac \
*.java \
owl/core/structure/*.java \
owl/core/structure/graphs/*.java \
owl/core/structure/scoring/*.java \
owl/core/sequence/*.java  \
owl/core/sequence/alignment/*.java \
owl/core/util/*.java  \
owl/core/util/actionTools/*.java \
owl/core/connections/*.java \
owl/core/connections/pisa/*.java \
owl/core/features/*.java \
owl/core/runners/*.java \
owl/core/runners/blast/*.java \
owl/core/runners/tinker/*.java 

# creating jar file
echo "Creating jar file: $tag.jar ..."
jar -cfm ../../$tag.jar ../Manifest.txt .

# removing $tag temp directory
cd ../..
rm -rf $tag
Revision:	1371
Committed:	Wed Mar 30 07:34:06 2011 UTC (9 years, 2 months ago) by jmduarteg
File size:	1504 byte(s)
Log Message:	Tagging owl-1.9.3 before major interface change.
Line	User	Rev	File contents
1	duarte	496	#!/bin/sh
2	duarte	971	if [ -z "$2" ]
3	duarte	496	then
4	jmduarteg	1261	echo "Usage: make-owl.sh <svn url> <tempdir> [<rev>]"
5			echo "e.g. for svn url: svn://black/aglappe/trunk or svn://bioinformatics.org/svnroot/owl/tags/owl-1.2.0"
6			echo "Optionally specify a revision to be exported instead of head"
7	duarte	496	exit
8			fi
9
10	duarte	971	svnurl=$1
11	duarte	968	tempdir=$2
12	jmduarteg	1261	rev=""
13			if [ -n "$3" ]
14			then
15			rev=$3
16			fi
17	duarte	496
18	duarte	968	echo "Compiling with:"
19			javac -version
20			echo ""
21	duarte	496
22
23			cd $tempdir
24
25	duarte	971	tag=`basename $svnurl`
26	duarte	496
27	jmduarteg	1261	revStr=""
28			if [ -n "$rev" ]
29			then
30			revStr="-r $rev"
31			fi
32	duarte	971
33	duarte	496	# exporting from svn
34			echo "Exporting source from svn"
35	jmduarteg	1261	svn export $revStr $svnurl
36	duarte	971	if [ "$?" -ne "0" ]
37	duarte	496	then
38	duarte	971	echo "Couldn't export from svn. Exiting"
39			exit 1
40	duarte	496	fi
41
42
43			# compiling
44			echo "Compiling..."
45	duarte	968	cd $tag/src
46	duarte	971
47
48			jarfiles=`ls ../jars/*.jar`
49			CLASSPATH="."
50			for jarfile in $jarfiles
51			do
52			CLASSPATH="$jarfile:$CLASSPATH"
53			done
54	jmduarteg	1152	jarfiles=`ls ../jars/uniprot/*.jar`
55			for jarfile in $jarfiles
56			do
57			CLASSPATH="$jarfile:$CLASSPATH"
58			done
59	duarte	971
60			echo $CLASSPATH
61
62
63	jmduarteg	1152	javac \
64			*.java \
65			owl/core/structure/*.java \
66	jmduarteg	1156	owl/core/structure/graphs/*.java \
67			owl/core/structure/scoring/*.java \
68	jmduarteg	1152	owl/core/sequence/*.java \
69	jmduarteg	1156	owl/core/sequence/alignment/*.java \
70	jmduarteg	1152	owl/core/util/*.java \
71	jmduarteg	1156	owl/core/util/actionTools/*.java \
72	jmduarteg	1152	owl/core/connections/*.java \
73	jmduarteg	1156	owl/core/connections/pisa/*.java \
74	jmduarteg	1152	owl/core/features/*.java \
75	jmduarteg	1156	owl/core/runners/*.java \
76			owl/core/runners/blast/*.java \
77			owl/core/runners/tinker/*.java
78	duarte	496
79			# creating jar file
80	duarte	968	echo "Creating jar file: $tag.jar ..."
81			jar -cfm ../../$tag.jar ../Manifest.txt .
82	duarte	496
83	duarte	968	# removing $tag temp directory
84			cd ../..
85	duarte	972	rm -rf $tag