src/hg/makeDb/trackDb/makefile 1.283

Index: src/hg/makeDb/trackDb/makefile
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/makefile,v
retrieving revision 1.282
retrieving revision 1.283
diff -b -B -U 1000000 -r1.282 -r1.283
--- src/hg/makeDb/trackDb/makefile	6 Jan 2010 21:45:10 -0000	1.282
+++ src/hg/makeDb/trackDb/makefile	6 Feb 2010 00:26:39 -0000	1.283
@@ -1,145 +1,145 @@
 # Make your private trackDb with 
 #	make update
 # Your private trackDb with additional options, for example:
 #       make EXTRA="-strict -settings" update
 # Make it for genome-test with
 #	make alpha
 # Make your private trackDb on local host (if defined as localDB.XXX=XXX in .hg.conf) with
 #	make updateLocal  
 # Make non-private trackDb on local host (if defined as localDB.XXX=XXX in .hg.conf) with
 #	make alphaLocal  
 # Make for ENCODE reporting (includes release alpha and release beta)
 #	make encodeReport
 
 # Browser supports multiple trackDb's so that individual developers
 # can change things rapidly without stepping on other people's toes. 
 # Usually when updating it is best to update your own trackDb and
 # test it to make sure it works and that you have cvs updated all
 # of trackDb/ before doing a make alpha. Note that you
 # must specify which trackDb you are using in your .hg.conf file
 # or in the cgi-bin-$(USER)/hg.conf file. Something like: 
 # db.trackDb=trackDb_YourUserName
 
 # note:  new group ARCHIVED_DBS created for assemblies still needed
 # to support Conservation tracks in other assemblies.  These should
 # have only chromInfo table on hgwbeta and RR.  make will not rebuild
 # trackDb on hgwdev unless the db is specified explicitly on the 
 # command line.
 
 include ../../../inc/common.mk
 
 DBS = 	hg16 hg17 hg18 hg19 hg19Haps \
 	venter1 \
 	panTro1 panTro2 \
 	gorGor1 gorGor2 \
 	ponAbe2 \
 	rheMac2 \
 	papHam1 \
 	macEug1 \
-	calJac1 \
+	calJac1 calJac3 \
 	otoGar1 tupBel1\
 	ailMel1 \
 	canFam1 canFam2 canFamPoodle1 \
 	felCat3 \
 	mm6 mm7 mm8 mm9 \
 	rn3 rn4 \
 	speTri1 cavPor3 \
 	oryCun1 oryCun2 \
 	bosTau2 bosTau3 bosTau4 \
 	equCab1 \
 	equCab2 \
 	eriEur1 sorAra1 susScr1 turTru1 vicVic1 pteVam1 tarSyr1 \
 	dipOrd1 proCap1 ochPri2 myoLuc1 \
 	micMur1 \
 	dasNov1 dasNov2 \
 	loxAfr1 loxAfr2 loxAfr3 \
 	echTel1 \
 	monDom1 monDom4 monDom5 \
 	anoCar1 \
 	galGal2 galGal3 \
 	taeGut1 \
 	xenTro1 xenTro2 \
 	tetNig1 tetNig2 \
 	oryLat1 oryLat2 \
 	ornAna1 \
 	fr1 fr2 \
 	petMar1 \
 	braFlo1 \
 	cioSav1 \
 	danRer3 danRer4 danRer5 danRer6\
 	gasAcu1 \
 	dm1 dm2 dm3 \
 	dp2 dp3 \
 	droYak1 droYak2 \
 	droAna1 droAna2 \
 	droMoj1 droMoj2 \
 	droVir1 droVir2 \
 	droEre1 \
 	droSim1 \
 	droGri1 \
 	droPer1 \
 	droSec1 \
 	anoGam1 \
 	apiMel1 \
 	apiMel2	\
 	triCas2 \
 	ci1 ci2 cioSav2 \
 	strPur1 strPur2 \
     nemVec1 \
 	aplCal1 \
 	ce2 ce3 ce4 ce5 ce6 ce7 ce8 \
 	cb1 cb2 cb3 \
 	caeRem1 caeRem2 caeRem3 \
 	caeJap1 caeJap2 \
 	priPac1 \
 	caePb1 caePb2 \
 	falciparum \
 	choHof1 \
 	sacCer1 sacCer2 \
 	sc1 \
 	h1n1 
 
 GSID_DBS = \
 	hiv1 vax004 hivgne8 hivmn hivmn1 hivmn2 hivgne8v2 hivVax003Vax004
 
 ARCHIVED_DBS = \
 	rheMac1 \
 	danRer1 \
 	mm5 \
 	mm6 \
 	danRer2
 
 update: #clean
 	./loadTracks ${EXTRA} trackDb_${USER} hgFindSpec_${USER} ${DBS}
 
 alpha: clean
 	${CVS} -q up -d -P .
 	./loadTracks -release=alpha trackDb hgFindSpec ${DBS}
 
 strict: clean
 	${CVS} -q up -d -P .
 	./loadTracks -strict -release=beta trackDb hgFindSpec ${DBS}
 
 # this will fail if we are not in a beta checkout:
 checkbeta:
 	${CVS} status trackDb.ra | egrep 'v[0-9]+_branch' > /dev/null
 
 beta: checkbeta clean strict
 
 encodeReport:
 	${CVS} -q up -d -P .
 	./loadTracks trackDb_encodeReport hgFindSpec ${DBS}
 
 listDbs:
 	@echo "# databases listed in trackDb/makefile DBS variable, with table counts"
 	@for D in ${DBS}; do \
 	    C=`hgsql -N -e "show tables;" $${D} 2> /dev/null | wc -l`; \
 	    if [ "$${C}" -gt 0 ]; then \
 		echo -e "$${D}\t$${C}"; \
 	    fi \
 	done
 
 # Get rid of symbolic links (created by lower-level makefiles):
 clean:
 	find . -type l -exec rm {} \;