1# =========================================================================== 2# 3# PUBLIC DOMAIN NOTICE 4# National Center for Biotechnology Information 5# 6# This software/database is a "United States Government Work" under the 7# terms of the United States Copyright Act. It was written as part of 8# the author's official duties as a United States Government employee and 9# thus cannot be copyrighted. This software/database is freely available 10# to the public for use. The National Library of Medicine and the U.S. 11# Government have not placed any restriction on its use or reproduction. 12# 13# Although all reasonable efforts have been taken to ensure the accuracy 14# and reliability of the software and data, the NLM and the U.S. 15# Government do not and cannot warrant the performance or results that 16# may be obtained by using this software or data. The NLM and the U.S. 17# Government disclaim all warranties, express or implied, including 18# warranties of performance, merchantability or fitness for any particular 19# purpose. 20# 21# Please cite the author in any work or product based on this material. 22# 23# =========================================================================== 24 25 26default: std 27 28TOP ?= $(abspath ../../../../../../..) 29MODULE = ngs/ngs-java/gov/nih/nlm/ncbi/ngs 30 31JARS = \ 32 ngs-ncbi.jar 33 34ALL_TARGS = \ 35 $(JARS) 36 37# default settings for java do not work here, override 38CLSPATH = $(TARGDIR)/ngs/ngs-java 39JAVASOURCEPATH = $(TOP)/ngs/ngs-java 40include $(TOP)/build/Makefile.env 41#$(warning JMAKE_CMD=$(JMAKE_CMD)) 42 43#------------------------------------------------------------------------------- 44# outer targets 45# 46all std: $(ALL_TARGS) 47 48$(JARS): makejdirs 49 @ $(JMAKE_CMD) $(CLSPATH)/$@ 50 51.PHONY: all std $(ALL_TARGS) 52 53#------------------------------------------------------------------------------- 54# clean 55# 56clean: stdjclean 57 58.PHONY: clean 59 60#------------------------------------------------------------------------------- 61# classes for ngs-ncbi 62# 63 64LIB_SRC = \ 65 HttpException \ 66 HttpManager \ 67 LibManager \ 68 LibPathIterator \ 69 Logger \ 70 Manager \ 71 ReadCollectionItf \ 72 Refcount \ 73 ReadGroupIteratorItf \ 74 ReadGroupItf \ 75 ReferenceIteratorItf \ 76 ReferenceItf \ 77 AlignmentItf \ 78 AlignmentIteratorItf \ 79 ReadItf \ 80 ReadIteratorItf \ 81 PileupIteratorItf \ 82 PileupItf \ 83 FragmentItf \ 84 PileupEventIteratorItf \ 85 PileupEventItf \ 86 TestyTheBear \ 87 88NGS_SRC = \ 89 NGS \ 90 $(LIB_SRC) 91 92#VARS = -Dvdb.System.loadLibrary=1 93#VARS = -Dvdb.log=FINEST 94#J=/net/pan1/sra-test/local/jdk1.7.0_51/bin/ 95#JAVABITS=-d$(BITS) 96 97$(SRCDIR)/NGS.java: \ 98 $(addprefix $(SRCDIR)/,$(addsuffix .java,$(LIB_SRC))) 99 100NGS_CLS = \ 101 $(addsuffix .class,$(NGS_SRC)) 102 103$(CLSPATH)/ngs-ncbi.jar: $(NGS_CLS) 104 ( cd $(CLSPATH); jar -cf $@ `find ngs gov -name *.class` ) 105 106#------------------------------------------------------------------------------- 107# manual integration test 108# 109test: $(CLSPATH)/ngs-ncbi.jar 110 cd $(CLSPATH); $(J)java $(JAVABITS) -classpath ngs-ncbi.jar $(VARS) \ 111 -Djava.library.path=$(LIBDIR) gov.nih.nlm.ncbi.ngs.TestyTheBear 112