#!/bin/bash

# NB: Run "mvn assembly:assembly" first to build the complete Jar2Lib JAR file.

JAR2LIB_DIR=`cd "$(dirname $0)/.."; pwd`
ARTIFACT_DIR=~/code/LOCI/java/artifacts
java -jar "$JAR2LIB_DIR/target/jar2lib-1.0-SNAPSHOT-deps.jar" \
  bfcpp "Bio-Formats C++ bindings" \
  $ARTIFACT_DIR/loci-common.jar \
  $ARTIFACT_DIR/ome-xml.jar \
  $ARTIFACT_DIR/bio-formats.jar \
  $ARTIFACT_DIR/flow-cytometry.jar \
  -conflicts $JAR2LIB_DIR/bf-cpp/conflicts.txt \
  -header $JAR2LIB_DIR/bf-cpp/header.txt

#!/bin/bash

# NB: Run "mvn assembly:assembly" first to build the complete Jar2Lib JAR file.

JAR2LIB_DIR=`cd "$(dirname $0)/.."; pwd`
REPOSITORY_DIR=~/.m2/repository

java -cp \
"$JAR2LIB_DIR/target/jar2lib-1.0-SNAPSHOT-deps.jar":\
"$REPOSITORY_DIR/imagej/ij/1.43/ij-1.43.jar":\
"$REPOSITORY_DIR/log4j/log4j/1.2.15/log4j-1.2.15.jar" \
  loci.jar2lib.Jar2Lib \
  bfcpp "Bio-Formats C++ bindings" \
  $REPOSITORY_DIR/loci/loci-common/5.0-SNAPSHOT/loci-common-5.0-SNAPSHOT.jar \
  $REPOSITORY_DIR/loci/loci_plugins/5.0-SNAPSHOT/loci_plugins-5.0-SNAPSHOT.jar \
  $REPOSITORY_DIR/loci/ome-xml/5.0-SNAPSHOT/ome-xml-5.0-SNAPSHOT.jar \
  $REPOSITORY_DIR/loci/bio-formats/5.0-SNAPSHOT/bio-formats-5.0-SNAPSHOT.jar \
  $REPOSITORY_DIR/loci/flow-cytometry/1.0-SNAPSHOT/flow-cytometry-1.0-SNAPSHOT.jar \
  -conflicts $JAR2LIB_DIR/bf-cpp/conflicts.txt \
  -header $JAR2LIB_DIR/bf-cpp/header.txt

Update bf-cpp invocation script: * Add loci_plugins library to the mix. * Point to JARs in local Maven repository.
Update bf-cpp invocation script:
  * Add loci_plugins library to the mix.
  * Point to JARs in local Maven repository.


