Skip to content
Snippets Groups Projects
Normal view Permalink
Makefile 13.5 KiB
Newer Older
tjc's avatar
J2 version
tjc committed
1 2 
# This is a GNU Makefile for Artemis
tjc's avatar
add picard libs  
tjc committed
3 
# $Header: //tmp/pathsoft/artemis/Makefile,v 1.47 2009-09-21 15:32:03 tjc Exp $
tjc's avatar
J2 version
tjc committed
4 5 6 

SHELL=/bin/sh
tjc's avatar
take out -g -deprecation compile flags  
tjc committed
7 
#OPT_FLAGS = -g -deprecation
tjc's avatar
J2 version
tjc committed
8
tjc's avatar
set target as 1.5  
tjc committed
9 
JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS)
tjc's avatar
J2 version
tjc committed
10
tcarver's avatar
add batik libs  
tcarver committed
11 
REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
tjc's avatar
J2 version
tjc committed
12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 

NAMES:= \
	uk/ac/sanger/artemis/OptionChangeListener \
	uk/ac/sanger/artemis/OptionChangeEvent \
	uk/ac/sanger/artemis/Options \
	uk/ac/sanger/artemis/Selection \
	uk/ac/sanger/artemis/components/ArtemisMain \
        uk/ac/sanger/artemis/components/ActMain \
	uk/ac/sanger/artemis/components/Splash \
	uk/ac/sanger/artemis/components/ListDialog \
	uk/ac/sanger/artemis/components/FeatureListFrame \
	uk/ac/sanger/artemis/components/FeatureList \
	uk/ac/sanger/artemis/components/FeatureDisplay \
	uk/ac/sanger/artemis/components/CanvasPanel \
	uk/ac/sanger/artemis/components/EntryGroupDisplay \
	uk/ac/sanger/artemis/components/EntryHeaderEdit \
	uk/ac/sanger/artemis/components/BasePlotGroup \
	uk/ac/sanger/artemis/components/EntryEditVector \
	uk/ac/sanger/artemis/components/EntryEdit \
	uk/ac/sanger/artemis/components/WritableEMBLCorbaEntrySource \
	uk/ac/sanger/artemis/components/DbfetchEntrySource \
	uk/ac/sanger/artemis/components/EMBLCorbaEntrySource \
	uk/ac/sanger/artemis/components/CorbaEntrySource \
	uk/ac/sanger/artemis/components/BioJavaEntrySource \
	uk/ac/sanger/artemis/components/FileDialogEntrySource \
	uk/ac/sanger/artemis/components/EntryActionListener \
	uk/ac/sanger/artemis/components/DisplayComponent \
	uk/ac/sanger/artemis/components/EntryFileDialog \
	uk/ac/sanger/artemis/components/StickyFileChooser \
	uk/ac/sanger/artemis/components/LogReadListener \
	uk/ac/sanger/artemis/components/Selector \
	uk/ac/sanger/artemis/components/Navigator \
	uk/ac/sanger/artemis/components/EntryGroupPanel \
	uk/ac/sanger/artemis/components/FeaturePopup \
	uk/ac/sanger/artemis/components/WriteMenu \
	uk/ac/sanger/artemis/components/SelectMenu \
	uk/ac/sanger/artemis/components/GraphMenu \
	uk/ac/sanger/artemis/components/RunMenu \
	uk/ac/sanger/artemis/components/AddMenu \
	uk/ac/sanger/artemis/components/ViewMenu \
	uk/ac/sanger/artemis/components/GotoMenu \
	uk/ac/sanger/artemis/components/EditMenu \
	uk/ac/sanger/artemis/components/SelectionMenu \
	uk/ac/sanger/artemis/components/SelectionViewer \
	uk/ac/sanger/artemis/components/FeaturePlotGroup \
	uk/ac/sanger/artemis/components/FeaturePlot \
	uk/ac/sanger/artemis/components/FeatureEdit \
	uk/ac/sanger/artemis/components/FeatureViewer \
	uk/ac/sanger/artemis/components/SearchResultViewer \
	uk/ac/sanger/artemis/components/LogViewer \
	uk/ac/sanger/artemis/components/FileViewer \
	uk/ac/sanger/artemis/components/MessageFrame \
	uk/ac/sanger/artemis/components/MessageDialog \
	uk/ac/sanger/artemis/components/YesNoDialog \
	uk/ac/sanger/artemis/components/KeyChooser \
	uk/ac/sanger/artemis/components/KeyChoice \
	uk/ac/sanger/artemis/components/QualifierEditor \
	uk/ac/sanger/artemis/components/QualifierTextArea \
	uk/ac/sanger/artemis/components/QualifierChoice \
	uk/ac/sanger/artemis/components/ChoiceFrame \
	uk/ac/sanger/artemis/components/SelectionInfoDisplay \
	uk/ac/sanger/artemis/components/EntryGroupMenu \
	uk/ac/sanger/artemis/components/EntryGroupInfoDisplay \
	uk/ac/sanger/artemis/components/Utilities \
	uk/ac/sanger/artemis/components/MarkerRangeRequester \
	uk/ac/sanger/artemis/components/MarkerRangeRequesterListener \
	uk/ac/sanger/artemis/components/MarkerRangeRequesterEvent \
	uk/ac/sanger/artemis/components/TextRequester \
	uk/ac/sanger/artemis/components/TextRequesterListener \
	uk/ac/sanger/artemis/components/TextRequesterEvent \
	uk/ac/sanger/artemis/components/TextDialog \
	uk/ac/sanger/artemis/components/BasePlot \
	uk/ac/sanger/artemis/components/ProcessWatcher \
	uk/ac/sanger/artemis/components/ProcessWatcherEvent \
	uk/ac/sanger/artemis/components/ProcessWatcherListener \
	uk/ac/sanger/artemis/components/ExternalProgramOptions \
	uk/ac/sanger/artemis/components/Plot \
	uk/ac/sanger/artemis/components/PlotMouseListener \
	uk/ac/sanger/artemis/components/FeatureAminoAcidViewer \
	uk/ac/sanger/artemis/components/FeatureBaseViewer \
	uk/ac/sanger/artemis/components/SequenceViewer \
	uk/ac/sanger/artemis/components/FeatureInfo \
	uk/ac/sanger/artemis/components/DisplayAdjustmentListener \
	uk/ac/sanger/artemis/components/DisplayAdjustmentEvent \
	uk/ac/sanger/artemis/components/ScoreChanger \
	uk/ac/sanger/artemis/components/ScoreScrollbar \
	uk/ac/sanger/artemis/components/ScoreChangeListener \
	uk/ac/sanger/artemis/components/ScoreChangeEvent \
	uk/ac/sanger/artemis/components/InputStreamProgressDialog \
	uk/ac/sanger/artemis/plot/KarlinSigAlgorithm \
	uk/ac/sanger/artemis/plot/UserDataAlgorithm \
	uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm \
	uk/ac/sanger/artemis/plot/ATDeviationAlgorithm \
	uk/ac/sanger/artemis/plot/GCDeviationAlgorithm \
	uk/ac/sanger/artemis/plot/GCFrameAlgorithm \
	uk/ac/sanger/artemis/plot/CodonUsageAlgorithm \
	uk/ac/sanger/artemis/plot/CodonUsageFormatException \
	uk/ac/sanger/artemis/plot/CodonUsageWeight \
	uk/ac/sanger/artemis/plot/CodonWeight \
	uk/ac/sanger/artemis/plot/AGWindowAlgorithm \
	uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm \
	uk/ac/sanger/artemis/plot/GCWindowAlgorithm \
	uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm \
	uk/ac/sanger/artemis/plot/HydroAlgorithm \
	uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm \
	uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm \
	uk/ac/sanger/artemis/plot/FeatureAlgorithm \
	uk/ac/sanger/artemis/plot/BaseAlgorithm \
	uk/ac/sanger/artemis/plot/Algorithm \
	uk/ac/sanger/artemis/Logger \
	uk/ac/sanger/artemis/ExternalProgramListener \
	uk/ac/sanger/artemis/ExternalProgramException \
	uk/ac/sanger/artemis/ExternalProgramVector \
	uk/ac/sanger/artemis/SimpleExternalProgramMonitor \
	uk/ac/sanger/artemis/ProcessMonitor \
	uk/ac/sanger/artemis/ProcessMonitor \
	uk/ac/sanger/artemis/ExternalProgramMonitor \
	uk/ac/sanger/artemis/ExternalProgram \
	uk/ac/sanger/artemis/EntryGroupChangeListener \
	uk/ac/sanger/artemis/EntryGroupChangeEvent \
	uk/ac/sanger/artemis/EntryChangeListener \
	uk/ac/sanger/artemis/EntryChangeEvent \
	uk/ac/sanger/artemis/FilteredEntryGroup \
	uk/ac/sanger/artemis/SimpleEntryGroup \
	uk/ac/sanger/artemis/EntryGroup \
	uk/ac/sanger/artemis/EntryVector \
	uk/ac/sanger/artemis/EntrySourceVector \
	uk/ac/sanger/artemis/EntrySource \
	uk/ac/sanger/artemis/Entry \
	uk/ac/sanger/artemis/LastSegmentException \
	uk/ac/sanger/artemis/FeatureFromVectorPredicate \
	uk/ac/sanger/artemis/FeatureKeyQualifierPredicate \
	uk/ac/sanger/artemis/FeatureKeyPredicate \
	uk/ac/sanger/artemis/FeaturePatternPredicate \
	uk/ac/sanger/artemis/FeaturePredicateConjunction \
	uk/ac/sanger/artemis/FeaturePredicate \
	uk/ac/sanger/artemis/FeaturePredicateVector \
	uk/ac/sanger/artemis/FeatureEnumeration \
	uk/ac/sanger/artemis/FeatureSegmentVector \
	uk/ac/sanger/artemis/FeatureChangeListener \
	uk/ac/sanger/artemis/FeatureChangeEvent \
	uk/ac/sanger/artemis/FeatureVector \
	uk/ac/sanger/artemis/Feature \
	uk/ac/sanger/artemis/FeatureSegment \
	uk/ac/sanger/artemis/ActionController \
	uk/ac/sanger/artemis/ActionVector \
	uk/ac/sanger/artemis/Action \
	uk/ac/sanger/artemis/ChangeListener \
	uk/ac/sanger/artemis/ChangeEventVector \
	uk/ac/sanger/artemis/ChangeEvent \
	uk/ac/sanger/artemis/GotoListener \
	uk/ac/sanger/artemis/GotoEvent \
	uk/ac/sanger/artemis/GotoEventSource \
	uk/ac/sanger/artemis/SimpleGotoEventSource \
	uk/ac/sanger/artemis/SelectionChangeListener \
	uk/ac/sanger/artemis/SelectionChangeEvent \
	uk/ac/sanger/artemis/Selectable \
	uk/ac/sanger/artemis/sequence/NoSequenceException \
	uk/ac/sanger/artemis/sequence/MarkerRangeVector \
	uk/ac/sanger/artemis/sequence/MarkerRange \
	uk/ac/sanger/artemis/sequence/MarkerChangeListener \
	uk/ac/sanger/artemis/sequence/MarkerChangeEvent \
	uk/ac/sanger/artemis/sequence/Marker \
	uk/ac/sanger/artemis/sequence/Strand \
	uk/ac/sanger/artemis/sequence/BasePatternFormatException \
	uk/ac/sanger/artemis/sequence/BasePattern \
	uk/ac/sanger/artemis/sequence/Bases \
	uk/ac/sanger/artemis/sequence/AminoAcidSequence \
	uk/ac/sanger/artemis/sequence/SequenceChangeListener \
	uk/ac/sanger/artemis/sequence/SequenceChangeEvent \
	uk/ac/sanger/artemis/io/BioJavaFeature \
	uk/ac/sanger/artemis/io/BioJavaSequence \
	uk/ac/sanger/artemis/io/BioJavaEntry \
	uk/ac/sanger/artemis/io/GenbankStreamSequence \
	uk/ac/sanger/artemis/io/RWCorbaEntry \
	uk/ac/sanger/artemis/io/CorbaEntry \
	uk/ac/sanger/artemis/io/DocumentEntryFactory \
	uk/ac/sanger/artemis/io/BlastDocumentEntry \
	uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry \
	uk/ac/sanger/artemis/io/GFFDocumentEntry \
	uk/ac/sanger/artemis/io/GenbankDocumentEntry \
	uk/ac/sanger/artemis/io/EmblDocumentEntry \
	uk/ac/sanger/artemis/io/PublicDBDocumentEntry \
	uk/ac/sanger/artemis/io/SimpleDocumentEntry \
	uk/ac/sanger/artemis/io/DocumentEntry \
	uk/ac/sanger/artemis/io/Entry \
	uk/ac/sanger/artemis/io/ReadOnlyEntry \
	uk/ac/sanger/artemis/io/QualifierInfoException \
	uk/ac/sanger/artemis/io/QualifierInfo \
	uk/ac/sanger/artemis/io/QualifierInfoVector \
	uk/ac/sanger/artemis/io/QualifierInfoHash \
tjc's avatar
compile circular plot  
tjc committed
203 
	uk/ac/sanger/artemis/chado/DbSqlConfig \
tjc's avatar
add digest  
tjc committed
204 205 206 
        uk/ac/sanger/artemis/circular/DNADraw \
	 uk/ac/sanger/artemis/circular/digest/Utils \
	uk/ac/sanger/artemis/circular/digest/CircularGenomeController
tjc's avatar
J2 version
tjc committed
207 208 209 210 211 212 213 214 215 

CLASSES := $(NAMES:%=%.class)
SOURCES := $(NAMES:%=%.java)

all: idl code

code: $(CLASSES)

topdown: idl
tjc's avatar
make file fixes  
tjc committed
216 
	$(REAL_CLASSPATH) $(JAVAC) uk/ac/sanger/artemis/components/ArtemisMain.java
tjc's avatar
J2 version
tjc committed
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 

%.class : %.java
	$(REAL_CLASSPATH) $(JAVAC) $<

idl : type/*.java nsdb/*.java seqdb/*.java

IDL = idlj
IDLCMD = $(IDL) -Icorba

type/*.java : corba/types.idl
	$(IDLCMD) corba/types.idl

nsdb/*.java : corba/nsdb.idl corba/nsdb_write.idl
	$(IDLCMD) corba/nsdb.idl
	$(IDLCMD) corba/nsdb_write.idl

seqdb/*.java : corba/seqdb.idl
	$(IDLCMD) corba/seqdb.idl

doc :
	$(REAL_CLASSPATH) javadoc -J-mx200m -version \
		AppGlobal.java \
		uk.ac.sanger.artemis uk.ac.sanger.artemis.components \
		uk.ac.sanger.artemis.sequence uk.ac.sanger.artemis.plot \
		uk.ac.sanger.artemis.util uk.ac.sanger.artemis.io

manual :
	(cd docs; make)

CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
tjc's avatar
remove jars chado and retrotranslator  
tjc committed
248 
OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README`
tjc's avatar
J2 version
tjc committed
249 250 251 252 253 254 

dist :
	rm -rf artemis_compiled.tar.gz tar_build
	mkdir tar_build
	mkdir tar_build/artemis
	rm -f artemis_compiled_latest.tar.gz
tcarver's avatar
add corba to dist  
tcarver committed
255 
	tar cf - $(OTHER_FILES) act art Makefile corba etc | (cd tar_build/artemis; tar xf -)
tjc's avatar
remove jars chado and retrotranslator  
tjc committed
256 
	tar cf - artemis_sqlmap dnaplotter uk org nsdb type seqdb lib | (cd tar_build/artemis; tar xf -)
tjc's avatar
remove .svn directories  
tjc committed
257 
	(cd tar_build; find . -name 'CVS' -print | xargs rm -rf; find . -name '.svn' -print | xargs rm -rf; tar cvf ../artemis_compiled.tar artemis)
tjc's avatar
J2 version
tjc committed
258
tjc's avatar
artemis act jars  
tjc committed
259 
jar : all artemis.jar
tjc's avatar
J2 version
tjc committed
260
tjc's avatar
artemis act jars  
tjc committed
261 262 263 264 
artemis.jar : $(CLASSES)
	mkdir jar_build
	rm -f artemis.jar
	cd jar_build; \
tjc's avatar
make file fixes  
tjc committed
265 
	if [ ! -d org ]; then \
tjc's avatar
artemis act jars  
tjc committed
266 267 268 
	  for fileJar in ../lib/*.jar; do \
	    jar xvf $$fileJar; \
	    rm -rf META-INF/MANIFEST.MF; \
tjc's avatar
make file fixes  
tjc committed
269 
	  done; \
tjc's avatar
add j2ssh to jar build  
tjc committed
270 271 272 
          for fileJar in ../lib/j2ssh/*.jar; do \
            jar xvf $$fileJar; \
            rm -rf META-INF/MANIFEST.MF; \
tjc's avatar
include ibatis jars in jar build  
tjc committed
273 274 275 276 
          done; \
          for fileJar in ../lib/ibatis/*.jar; do \
            jar xvf $$fileJar; \
            rm -rf META-INF/MANIFEST.MF; \
tjc's avatar
add j2ssh to jar build  
tjc committed
277 
          done; \
tcarver's avatar
update  
tcarver committed
278 279 280 281 
          for fileJar in ../lib/batik/*.jar; do \
            jar xvf $$fileJar; \
            rm -rf META-INF/MANIFEST.MF; \
          done; \
tjc's avatar
add picard to jar file  
tjc committed
282 283 284 285 
          for fileJar in ../lib/picard/*.jar; do \
            jar xvf $$fileJar; \
            rm -rf META-INF/MANIFEST.MF; \
          done; \
tjc's avatar
artemis act jars  
tjc committed
286 
        fi; \
tjc's avatar
remove jars chado and retrotranslator  
tjc committed
287 288 
	cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
	      ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
tjc's avatar
artemis act jars  
tjc committed
289 
	find jar_build -name '*.java' -print | xargs rm -f
tjc's avatar
add picard to jar file  
tjc committed
290 
	find jar_build -name '.svn' -print | xargs rm -rf
tjc's avatar
artemis act jars  
tjc committed
291 292 293 
	cd jar_build; \
	rm -rf META-INF/MANIFEST.MF; \
	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain" > manifest-art; \
tcarver's avatar
fix for svg  
tcarver committed
294 
	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
tjc's avatar
updates for chado  
tjc committed
295 
	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
tjc's avatar
make circular.jar  
tjc committed
296 
        echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw" > manifest-circular; \
tjc's avatar
DNAPlotter  
tjc committed
297 
        jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
tcarver's avatar
update  
tcarver committed
298 
                             uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
tjc's avatar
add BamView  
tjc committed
299 
	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView" > manifest-bamview; \
tcarver's avatar
fix for svg  
tcarver committed
300 
	jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
tjc's avatar
artemis act jars  
tjc committed
301 
	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain" > manifest-act; \
tcarver's avatar
fix for svg  
tcarver committed
302 
	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
tjc's avatar
updates for chado  
tjc committed
303 
	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
tjc's avatar
added artemis_mac.jar  
tjc committed
304 
	rm -f etc/log4j.properties; \
tjc's avatar
remove jars chado and retrotranslator  
tjc committed
305 306 
	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
	        uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
tjc's avatar
J2 version
tjc committed
307 308 

clean :
tjc's avatar
remove jars chado and retrotranslator  
tjc committed
309 
	-rm -rf *.html artemis.jar seqdb nsdb type resources uk/ac/sanger/jcon/ jar_build tar_build  artemis_compiled.tar
tjc's avatar
J2 version
tjc committed
310 311 
	-rm -rf TAGS* *.o
	-find . -name '*.class' -print | xargs rm -f