src/hg/near/hprdXmlToTab/makefile 1.1

1.1 2009/10/15 21:58:38 kent
Utility to convert HPRD interaction html file to tab-separated list of protein/protein interactions seems to work. This is based on an autoXml parser and a snippet of code Galt wrote that now lives in hprdXmlToTab.c.

Index: src/hg/near/hprdXmlToTab/makefile
===================================================================
RCS file: src/hg/near/hprdXmlToTab/makefile
diff -N src/hg/near/hprdXmlToTab/makefile
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/near/hprdXmlToTab/makefile	15 Oct 2009 21:58:38 -0000	1.1
@@ -0,0 +1,37 @@
+
+JKSRCDIR = $(HOME)/kent/src
+JKLIBDIR = $(JKSRCDIR)/lib/$(MACHTYPE)
+
+EXE = hprdXmlToTab
+
+.c.o:
+	gcc -ggdb -Wimplicit -DDEBUG -Wall -I$(JKSRCDIR)/inc -I$(JKSRCDIR)/hg/inc -c $*.c
+
+L = $(MYSQLLIBS) -lm
+MYLIBS = $(JKLIBDIR)/jkhgap.a $(JKLIBDIR)/jkweb.a 
+
+
+all: $(EXE)
+
+makeXmlParser: single-fixed.xml
+	autoDtd single-fixed.xml out.dtd out.stats -tree=out.tree -atree=out.atree
+	autoXml out.dtd hprd
+
+runXmlParser: hprdXmlToTab single-fixed.html
+	hprdXmlToTab single-fixed.xml hprd.p2p hprdComplex.tab
+
+test: hprd.p2p
+	hgNetDist hprd.p2p hg18 humanHprdP2P -weighted -threshold=2 -sqlRemap="select distinct value, name from knownToHprd"
+
+
+O = $(EXE).o
+
+$(EXE): $O hprd.o
+	gcc $O hprd.o $(MYLIBS) $L -o $(EXE)
+	chmod a+rx $(EXE)
+	strip $(EXE)
+	cp $(EXE) $(HOME)/bin/$(MACHTYPE)
+
+clean:
+	rm -f *.o $(EXE) 
+