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makefile.dev
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makefile.dev
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#############################################################################
# Copyright (c) Minh Duc Cao, Monash Uni & UQ, All rights reserved. #
# #
# Redistribution and use in source and binary forms, with or without #
# modification, are permitted provided that the following conditions #
# are met: #
# #
# 1. Redistributions of source code must retain the above copyright notice, #
# this list of conditions and the following disclaimer. #
# 2. Redistributions in binary form must reproduce the above copyright #
# notice, this list of conditions and the following disclaimer in the #
# documentation and/or other materials provided with the distribution. #
# 3. Neither the names of the institutions nor the names of the contributors#
# may be used to endorse or promote products derived from this software #
# without specific prior written permission. #
# #
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS #
# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, #
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR #
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR #
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, #
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, #
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR #
# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF #
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING #
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS #
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. #
############################################################################/
############################################################################
# A generic makefile for java
#
############################################################################
###########################################################################
# Modify the following parameter to suit your setting
#Class directory
CLASS_DIR=target/dev-classes
#Source directory
SRC_MAIN_DIR=src/main/java
SRC_DEV_DIR=src/dev/java
##SRC_WORK_DIR=src/work/java
#Java compiler
JCC=javac
#target jar file
JAR_FILE=japsa-dev.jar
#External library directory
LIB_DIR=libs
#List of external libraries
##EXT_LIBS=colloquial.jar commons-io-2.5.jar commons-math3-3.0.jar jhdf5.jar jhdfobj.jar htsjdk-2.10.1.jar guava-18.0.jar jcommon-1.0.23.jar jfreechart-1.0.19.jar JRIEngine.jar JRI.jar gs-core-1.3.jar gs-ui-1.3.jar gs-algo-1.3.jar javax.json-api-1.0.jar javax.json-1.0.4.jar slf4j-api-1.7.25.jar slf4j-simple-1.7.25.jar jfxrt.jar gson-2.3.jar
EXT_LIBS=pal1.5.1.1.jar mdsj.jar colloquial.jar commons-io-2.5.jar commons-math3-3.0.jar jhdf5.jar jhdfobj.jar htsjdk-2.10.1.jar guava-18.0.jar jcommon-1.0.23.jar jfreechart-1.0.19.jar gs-core-1.3.jar gs-ui-1.3.jar gs-algo-1.3.jar javax.json-api-1.0.jar javax.json-1.0.4.jar slf4j-api-1.7.25.jar slf4j-simple-1.7.25.jar jfxrt.jar gson-2.3.jar
#EXT_LIBS=pal1.5.1.1.jar mdsj.jar colloquial.jar commons-io-2.5.jar commons-math3-3.6.1.jar jhdf5.jar jhdfobj.jar htsjdk-2.18.2.jar guava-18.0.jar jcommon-1.0.23.jar jfreechart-1.0.19.jar gs-core-1.3.jar gs-ui-1.3.jar gs-algo-1.3.jar javax.json-api-1.0.jar javax.json-1.0.4.jar slf4j-api-1.7.25.jar slf4j-simple-1.7.25.jar jfxrt.jar gson-2.3.jar
###########################################################################
##What this scripts does:
# 1. Find all packages by searching SRC_DIR subdirectories
# 2. Get all the java file, and compile them to the CLASS_DIR directory
# 5. Clean back up files (*.bak, ~, etc)
# To be implemented:
# 3. Copy all the resources to class directory
# 4. Make java file
##########################################################################
COMMA:= ,
EMPTY:=
SPACE:= $(SPACE) $(SPACE)
LIBS:=$(subst $(SPACE),:, $(addprefix $(LIB_DIR)/, $(EXT_LIBS)))
##Get all the packages in $(SRC_MAIN_DIR).
PACKAGE_MAIN_DIRS := $(shell echo `cd $(SRC_MAIN_DIR);find . -type d`)
SRC_MAIN_DIRS := $(addprefix $(SRC_MAIN_DIR)/, $(PACKAGE_MAIN_DIRS))
CLASS_MAIN_DIRS := $(addprefix $(CLASS_DIR)/, $(PACKAGE_MAIN_DIRS))
##Get the list of java files
JAVA_MAIN_FILES := $(foreach dir,$(SRC_MAIN_DIRS),$(wildcard $(dir)/*.java))
CLASS_MAIN_FILES := $(subst $(SRC_MAIN_DIR)/,$(CLASS_DIR)/,$(JAVA_MAIN_FILES:.java=.class))
PACKAGE_DEV_DIRS := $(shell echo `cd $(SRC_DEV_DIR);find . -type d`)
SRC_DEV_DIRS := $(addprefix $(SRC_DEV_DIR)/, $(PACKAGE_DEV_DIRS))
CLASS_DEV_DIRS := $(addprefix $(CLASS_DIR)/, $(PACKAGE_DEV_DIRS))
##Get the list of java files
JAVA_DEV_FILES := $(foreach dir,$(SRC_DEV_DIRS),$(wildcard $(dir)/*.java))
CLASS_DEV_FILES := $(subst $(SRC_DEV_DIR)/,$(CLASS_DIR)/,$(JAVA_DEV_FILES:.java=.class))
#TODO: merge three src dirs to one by foreach
#####################Make targets
VPATH=$(subst ' ',':',$(PACKAGE_MAIN_DIRS))
$(CLASS_DIR)/%.class: $(SRC_MAIN_DIR)/%.java $(CLASS_DIR)
$(JCC) -sourcepath $(SRC_MAIN_DIR) -cp $(CLASS_DIR):$(LIBS) -nowarn -d $(CLASS_DIR) $(JDEBUGFLAGS) $<
VPATH=$(subst ' ',':',$(PACKAGE_DEV_DIRS))
$(CLASS_DIR)/%.class: $(SRC_DEV_DIR)/%.java $(CLASS_DIR)
$(JCC) -sourcepath $(SRC_DEV_DIR):$(SRC_MAIN_DIR) -cp $(CLASS_DIR):$(LIBS) -nowarn -d $(CLASS_DIR) $(JDEBUGFLAGS) $<
all: jar
main-classes: $(CLASS_MAIN_FILES)
dev-classes: $(CLASS_DEV_FILES)
###Create the class directory if neccessary
$(CLASS_DIR):
mkdir -p $(CLASS_DIR)
images:
cp -r $(SRC_MAIN_DIR)/japsa/bio/misc/dnaPlatform/gui/images $(CLASS_DIR)/japsa/bio/misc/dnaPlatform/gui/
cp -r $(SRC_MAIN_DIR)/japsa/seq/nanopore/icons $(CLASS_DIR)/japsa/seq/nanopore/
$(JAR_FILE): main-classes dev-classes images
jar cf $(JAR_FILE) -C $(CLASS_DIR) .
jar: $(JAR_FILE)
clean:
@@for i in $(PACKAGE_MAIN_DIRS); do \
echo "rm -f $(SRC_MAIN_DIR)/$$i/*.bak $(SRC_MAIN_DIR)/$$i/*.class $(SRC_MAIN_DIR)/$$i/*~ $(CLASS_DIR)/$$i/*.class"; \
rm -f $(SRC_MAIN_DIR)/$$i/*.bak $(SRC_MAIN_DIR)/$$i/*.class $(SRC_MAIN_DIR)/$$i/*~ $(CLASS_DIR)/$$i/*.class; \
done
@@for i in $(PACKAGE_DEV_DIRS); do \
echo "rm -f $(SRC_DEV_DIR)/$$i/*.bak $(SRC_DEV_DIR)/$$i/*.class $(SRC_DEV_DIR)/$$i/*~ $(CLASS_DIR)/$$i/*.class"; \
rm -f $(SRC_DEV_DIR)/$$i/*.bak $(SRC_DEV_DIR)/$$i/*.class $(SRC_DEV_DIR)/$$i/*~ $(CLASS_DIR)/$$i/*.class; \
done
rm -f install.sh install.bat
##############################################################################
# INSTALLATION
##############################################################################
ifdef INSTALL_DIR
O_INS_DIR=-installDir=\"${INSTALL_DIR}\"
else
O_INS_DIR=
endif
ifdef JLP
O_JLP=-jlp=\"${JLP}\"
else
O_JLP=
endif
ifdef MXMEM
O_MXMEM=-xmx=${MXMEM}
else
O_MXMEM=
endif
ifdef SERVER
O_SERVER=--server=${SERVER}
else
O_SERVER=
endif
##=/usr/lib/jni:/usr/lib/R/site-library/rJava/jri
pre-install: jar
@@echo "java -cp $(JAR_FILE):$(LIB_DIR)/guava-18.0.jar:$(LIB_DIR)/slf4j-api-1.7.25.jar:$(LIB_DIR)/slf4j-simple-1.7.25.jar japsadev.util.deploy.DevDeploy --mode install --libs $(subst $(SPACE),:, $(EXT_LIBS)) $(O_INS_DIR) $(O_JLP) $(O_MXMEM) $(O_SERVER) --compiler \"`$(JCC) -version 2>&1`\"" > install.sh && \
chmod u+x install.sh && \
echo "java -cp $(JAR_FILE):$(LIB_DIR)\guava-18.0.jar:$(LIB_DIR)/slf4j-api-1.7.25.jar:$(LIB_DIR)/slf4j-simple-1.7.25.jar japsadev.util.deploy.DevDeploy --mode install --libs $(subst $(SPACE),:, $(EXT_LIBS)) $(O_INS_DIR) $(O_JLP) $(O_MXMEM) $(O_SERVER)--compiler \"`$(JCC) -version 2>&1`\"" > install.bat &&\
echo "Installation scripts created"
install: pre-install
./install.sh
uninstall:
@@java -cp $(JAR_FILE):$(LIB_DIR)/guava-18.0.jar:$(LIB_DIR)/slf4j-api-1.7.25.jar:$(LIB_DIR)/slf4j-simple-1.7.25.jar japsadev.util.deploy.DevDeploy --mode uninstall --libs $(subst $(SPACE),:, $(EXT_LIBS)) ${O_INS_DIR} && echo "Japsa uninstalled!"
galaxy: jar
@@java -cp $(JAR_FILE):$(LIB_DIR)/guava-18.0.jar:$(LIB_DIR)/slf4j-api-1.7.25.jar:$(LIB_DIR)/slf4j-simple-1.7.25.jar japsadev.util.deploy.DevDeploy --mode galaxy && echo "Galaxy wrappers generated!"