Commit f38f870f authored by shubham mukherjee's avatar shubham mukherjee

build script

parent c85bb10b
......@@ -12,13 +12,13 @@ Note the path of the base directory where the gesall-core / gesall-htsjdk / gesa
After going into the gesall-core dir simply run 'build.sh' inserting the
```
$> ./build.sh -dir=<path-to-your-base-dir>
$> bash ./build.sh -dir=<path-to-your-base-dir>
```
#### What it does?
1. Replaces the path of your base directory in the Ant buils files to pickup the dependencies.
2. Uses ant_build/build_clean.xml and ant_build/build_clean.xml, to build Runnable jar files for the program.clean.latest and program.md.latest module respectively.
3. Package the program.alignment.latest into a jar file. Note that this is not directly runnable.
3. Package the program.alignment.latest into a jar file using the existing .class files in bin/ directory. Note that this is not directly runnable.
#### Output format
The directory out/ in the base directory contains the 3 jar files.
......
......@@ -2,10 +2,10 @@
<project default="create_run_jar" name="Create Runnable Jar for Project gesall-core">
<!--this file was created by Eclipse Runnable JAR Export Wizard-->
<!--ANT 1.7 is required -->
<property name="homedir" value="/home/shubham/geneproject" />
<property name="homedir" value="HOMEDIR" />
<target name="create_run_jar">
<jar destfile="${homedir}/gesall-core/test1.jar" filesetmanifest="mergewithoutmain">
<jar destfile="${homedir}/gesall-core/out/clean.jar" filesetmanifest="mergewithoutmain">
<manifest>
<!-- <attribute name="Main-Class" value="hdfs.clean.bam.bloom.md.MarkDuplicatesMain"/> -->
<attribute name="Main-Class" value="program.clean.latest.CleanMRMain"/>
......
......@@ -2,10 +2,10 @@
<project default="create_run_jar" name="Create Runnable Jar for Project gesall-core">
<!--this file was created by Eclipse Runnable JAR Export Wizard-->
<!--ANT 1.7 is required -->
<property name="homedir" value="/home/shubham/geneproject" />
<property name="homedir" value="HOMEDIR" />
<target name="create_run_jar">
<jar destfile="${homedir}/gesall-core/test1.jar" filesetmanifest="mergewithoutmain">
<jar destfile="${homedir}/gesall-core/out/md.jar" filesetmanifest="mergewithoutmain">
<manifest>
<!-- <attribute name="Main-Class" value="hdfs.clean.bam.bloom.md.MarkDuplicatesMain"/> -->
<attribute name="Main-Class" value="program.md.latest.MarkDuplicatesMain"/>
......
#!/bin/bash
if [[ $# -eq 0 || $# -gt 1 ]]
then
echo "Correct usage ./build.sh -d=<path-to-base-dir>"
exit 1
fi
for i in "$@"
do
case $i in
-d=*|--dir=*)
homedir="${i#*=}"
gesallcore=$homedir'/gesall-core'
shift # past argument=value
;;
--default)
DEFAULT=YES
shift # past argument with no value
;;
*)
echo "Correct usage ./build.sh -d=<path-to-base-dir>"
exit 1 # unknown option
;;
esac
done
# echo 'test '$homedir
# echo 'test 1' $gesallcore
sed -i "s@HOMEDIR@$homedir@" $gesallcore/ant-build/build_clean.xml
sed -i "s@HOMEDIR@$homedir@" $gesallcore/ant-build/build_md.xml
ant -f $gesallcore/ant-build/build_clean.xml
ant -f $gesallcore/ant-build/build_md.xml
cd $gesallcore/src/program/alignment/latest
rm -rf ./build
mkdir ./build
#javac -d ./build *.java
#cd ./build
cd $gesallcore/bin/program/alignment/latest
jar cvf aligment.jar *class
mv ./aligment.jar $gesallcore/out/
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment