From: <ds...@us...> - 2012-01-23 19:47:31
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Revision: 5717 http://sashimi.svn.sourceforge.net/sashimi/?rev=5717&view=rev Author: dshteyn Date: 2012-01-23 19:47:24 +0000 (Mon, 23 Jan 2012) Log Message: ----------- Build: Get the build to work under CentOS with xtandem and PepC compiling. Modified Paths: -------------- trunk/trans_proteomic_pipeline/src/Makefile Modified: trunk/trans_proteomic_pipeline/src/Makefile =================================================================== --- trunk/trans_proteomic_pipeline/src/Makefile 2012-01-23 19:45:09 UTC (rev 5716) +++ trunk/trans_proteomic_pipeline/src/Makefile 2012-01-23 19:47:24 UTC (rev 5717) @@ -243,6 +243,7 @@ Validation/PeptideProphet/PeptideProphetParser \ Validation/InterProphet/InterProphetParser \ Validation/PTMProphetParser \ + Validation/SRMProphet \ Visualization \ Visualization/Pep3D \ Visualization/Pep3D/cgi_Pep3D_xml \ @@ -262,11 +263,13 @@ # # targets # +#EXE_XML = $(OBJ_ARCH)/regenerate_VersionInfo \ EXE_XML = xtandem $(OBJ_ARCH)/regenerate_VersionInfo \ $(OBJ_ARCH)/PeptideProphetParser \ $(OBJ_ARCH)/InterProphetParser \ $(OBJ_ARCH)/PTMProphetParser \ + $(OBJ_ARCH)/SRMProphet \ $(OBJ_ARCH)/RTCalc \ $(OBJ_ARCH)/RTCatalogParser \ $(OBJ_ARCH)/ProteinProphet \ @@ -484,11 +487,11 @@ @if [ ! -e ../extern/json/json.xml ]; then cd ../extern; tar -xzf json.tgz; fi; @if [ ! -e ../extern/jfreechart-1.0.9/lib/jfreechart-1.0.9.jar ]; then cd ../extern; tar -xzf jfreechart109.tgz; fi; @if [ ! -e ../extern/GWT/gwt-dev.jar ]; then cd ../extern; rm -rf GWT ; rm -rf gwt ; tar -xzf GWT.tgz; fi; - which $(ANT_EXE) ; if [ $$? -eq 0 ] ; then \ + #which $(ANT_EXE) ; if [ $$? -eq 0 ] ; then \ export CLASSPATH="" ; $(ANT_EXE_PRE) $(ANT_EXE) -f ../extern/json/json.xml compile.module.json $(ANT_EXE_POST) ; \ export CLASSPATH="" ; $(ANT_EXE_PRE) $(ANT_EXE) -f Quantitation/Pepc/build.xml jar $(ANT_EXE_POST) ; \ cp -f Quantitation/Pepc/Pepc.jar $(OBJ_ARCH); \ - fi ; + #fi ; _PepcView : $(OBJ_ARCH)/PepcView/PepcView.html @@ -496,13 +499,13 @@ @if [ ! -e ../extern/json/json.xml ]; then cd ../extern; tar -xzf json.tgz; fi; @if [ ! -e ../extern/jfreechart-1.0.9/lib/jfreechart-1.0.9.jar ]; then cd ../extern; tar -xzf jfreechart109.tgz; fi; @if [ ! -e ../extern/GWT/gwt-dev.jar ]; then cd ../extern; rm -rf GWT ; rm -rf gwt ; tar -xzf GWT.tgz; fi; - which $(ANT_EXE) ; if [ $$? -eq 0 ] ; then \ + #which $(ANT_EXE) ; if [ $$? -eq 0 ] ; then \ rm -rf Quantitation/Pepc/PepcView/GWTCompilerOutputpepcview/com.insilicos.PepcView/* ; \ export CLASSPATH="" ; $(ANT_EXE_PRE) $(ANT_EXE) -f Quantitation/Pepc/PepcView/build.xml compile.gwt.pepcview $(ANT_EXE_POST) ; \ mkdir -p $(OBJ_ARCH)/PepcView ; \ rm -f $(OBJ_ARCH)/PepcView/* ; \ cp -f Quantitation/Pepc/PepcView/GWTCompilerOutputpepcview/com.insilicos.PepcView/* $(OBJ_ARCH)/PepcView ; \ - fi ; + #fi ; info : @@ -545,6 +548,8 @@ $(OBJ_ARCH)/PTMProphetParser.o \ $(OBJ_ARCH)/PTMProphetMain.o \ $(OBJ_ARCH)/PTMProphet.o \ + $(OBJ_ARCH)/SRMProphetMain.o \ + $(OBJ_ARCH)/SRMProphet.o \ $(OBJ_ARCH)/RTCatalog.o \ $(OBJ_ARCH)/GradientProgram.o \ $(OBJ_ARCH)/RTCatalogParser.o \ @@ -667,6 +672,8 @@ _PTMProphetParser : $(OBJ_ARCH)/PTMProphetParser +_SRMProphet : $(OBJ_ARCH)/SRMProphet + _RTCalc : $(OBJ_ARCH)/RTCalc _RTCatalogParser : $(OBJ_ARCH)/RTCatalogParser @@ -677,6 +684,9 @@ $(OBJ_ARCH)/PTMProphetParser: $(OBJ_ARCH)/PTMProphetMain.o $(OBJ_ARCH)/KDModel.o $(OBJ_ARCH)/PTMProphet.o $(OBJ_ARCH)/PTMProphetParser.o $(TPPLIB) $(SPECTRAST_LIB) $(LD) $(DEBUG) $(OPT) -o $@ $^ $(LDFLAGS) +$(OBJ_ARCH)/SRMProphet: $(OBJ_ARCH)/SRMProphetMain.o $(OBJ_ARCH)/KDModel.o $(OBJ_ARCH)/SRMProphet.o $(TPPLIB) $(SPECTRAST_LIB) + $(LD) $(DEBUG) $(OPT) -o $@ $^ $(LDFLAGS) + #$(OBJ_ARCH)/SpectraSTPepXMLLibImporter.o : $(OBJ_ARCH)/XMLWalker.o $(OBJ_ARCH)/FileUtils.o $(OBJ_ARCH)/RTCalc: $(OBJ_ARCH)/RTCalculatorMain.o $(TPPLIB) @@ -907,7 +917,7 @@ _Tandem2XML : $(OBJ_ARCH)/Tandem2XML -$(OBJ_ARCH)/Tandem2XML : $(OBJ_ARCH)/Tandem2xml.o $(OBJ_ARCH)/TandemParamsParser.o $(OBJ_ARCH)/TandemResultsParser.o $(OBJ_ARCH)/masscalc.o $(OBJ_ARCH)/saxtandemhandler.o $(TPPLIB) $(OBJ_ARCH)/libexpat.a +$(OBJ_ARCH)/Tandem2XML : $(OBJ_ARCH)/Tandem2xml.o $(OBJ_ARCH)/TandemParamsParser.o $(OBJ_ARCH)/TandemResultsParser.o $(OBJ_ARCH)/masscalc.o $(OBJ_ARCH)/saxtandemhandler.o $(TPPLIB) $(EXPAT_LIB) $(LD) $(DEBUG) $(OPT) -o $@ $^ $(LDFLAGS) _comet-fastadb.cgi : $(OBJ_ARCH)/comet-fastadb.cgi @@ -1085,13 +1095,13 @@ XTANDEM_SRCDIR = ../extern/xtandem/src xtandem: $(EXPAT_LIB) $(GZSTREAMLIB) $(LIB_PWIZ) $(OBJ_ARCH)/TPPVersionInfo.o - make -C $(XTANDEM_SRCDIR) TANDEM_PARAMETERS_INSTALL_DIR="${TANDEM_PARAMETERS_INSTALL_DIR}" SRC_ROOT="$(SRC_ROOT)" ARCH=$(ARCH) BUILD_DIR=$(OBJ_ARCH) EXPAT_LIB=$(OBJ_ARCH)/libexpat.a ZLIB_INCL="$(ZLIB_INCL)" ZLIB_LIB="$(ZLIB_LIB)" USER_OBJS="$(OBJ_ARCH)/TPPVersionInfo.o" + make -C $(XTANDEM_SRCDIR) TANDEM_PARAMETERS_INSTALL_DIR="${TANDEM_PARAMETERS_INSTALL_DIR}" SRC_ROOT="$(SRC_ROOT)" ARCH=$(ARCH) BUILD_DIR=$(OBJ_ARCH) EXPAT_LIB=$(EXPAT_LIB) ZLIB_INCL="$(ZLIB_INCL)" ZLIB_LIB="$(ZLIB_LIB)" USER_OBJS="$(OBJ_ARCH)/TPPVersionInfo.o" # target for building our version of the MPI-parallelized X!!Tandem bbtandem: $(EXPAT_LIB) $(GZSTREAMLIB) $(LIB_PWIZ) $(OBJ_ARCH)/TPPVersionInfo.o - make -C $(XTANDEM_SRCDIR) XBANGBANG=1 TANDEM_PARAMETERS_INSTALL_DIR="${TANDEM_PARAMETERS_INSTALL_DIR}" SRC_ROOT="$(SRC_ROOT)" ARCH=$(ARCH) BUILD_DIR=$(OBJ_ARCH) EXPAT_LIB=$(OBJ_ARCH)/libexpat.a ZLIB_INCL="$(ZLIB_INCL)" ZLIB_LIB="$(ZLIB_LIB)" USER_OBJS="$(OBJ_ARCH)/TPPVersionInfo.o" + make -C $(XTANDEM_SRCDIR) XBANGBANG=1 TANDEM_PARAMETERS_INSTALL_DIR="${TANDEM_PARAMETERS_INSTALL_DIR}" SRC_ROOT="$(SRC_ROOT)" ARCH=$(ARCH) BUILD_DIR=$(OBJ_ARCH) EXPAT_LIB=$(EXPAT_LIB) ZLIB_INCL="$(ZLIB_INCL)" ZLIB_LIB="$(ZLIB_LIB)" USER_OBJS="$(OBJ_ARCH)/TPPVersionInfo.o" xtandem-clean: make -C $(XTANDEM_SRCDIR) SRC_ROOT="$(SRC_ROOT)" ARCH=$(ARCH) BUILD_DIR=$(OBJ_ARCH) clean @@ -1128,6 +1138,7 @@ cp -f ../CGI/*.pl `cygpath -u $$WEBSERVER_ROOT`/../tpp-bin cp -f ../HELP_DIR/*.* `cygpath -u $$WEBSERVER_ROOT`/../tpp-bin cp -f ../images/*.* `cygpath -u $$WEBSERVER_ROOT`/../tpp-bin + cp -f ../extern/d3/*.js `cygpath -u $$WEBSERVER_ROOT`/ISB/html/js sed -i 's?/tpp/cgi-bin/?/tpp-bin/?g' `cygpath -u $$WEBSERVER_ROOT`/pepXML_std.xsl chmod -R a+xr `cygpath -u $$WEBSERVER_ROOT`/../tpp-bin cp -f Visualization/Comet/cometlinks.def `cygpath -u $$WEBSERVER_ROOT` @@ -1700,6 +1711,8 @@ cp -f $(OBJ_ARCH)/XPressPeptideUpdateParser.cgi ${CGI_DIR} cp -f $(OBJ_ARCH)/plotspectrast.cgi ${CGI_DIR} cp -f $(OBJ_ARCH)/TPPVersionInfo.pl ${CGI_DIR} + cp -f ../extern/d3/*.js ${CGI_DIR} + cp -f $(OBJ_ARCH)/TPPVersionInfo.pl ${CGI_DIR} if [ -e $(OBJ_ARCH)/PepcView ]; then cp -fr $(OBJ_ARCH)/PepcView ${CGI_DIR} ; chmod -R a+x $(CGI_DIR)PepcView ; fi; chmod a+x ${CGI_DIR}* chmod -R a+rw ${CGI_USERS_DIR} @@ -1729,6 +1742,7 @@ cp -f $(OBJ_ARCH)/ProteinProphet ${BIN_DIR} cp -f $(OBJ_ARCH)/TPPVersionInfo.pl ${BIN_DIR} cp -f $(OBJ_ARCH)/TPPVersionInfo.pl ${CGI_DIR} + cp -f ../extern/d3/*.js ${CGI_DIR}/../html/js cp -f $(OBJ_ARCH)/StatUtilities.pm ${BIN_DIR} cp -f $(OBJ_ARCH)/calctppstat.pl ${BIN_DIR} cp -f $(OBJ_ARCH)/StatUtilities.pm ${CGI_DIR} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |