src/hg/makeDb/doc/panTro2.txt 1.14

Index: src/hg/makeDb/doc/panTro2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/panTro2.txt,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 4 -r1.13 -r1.14
--- src/hg/makeDb/doc/panTro2.txt	17 Oct 2008 01:06:35 -0000	1.13
+++ src/hg/makeDb/doc/panTro2.txt	27 Apr 2009 20:10:57 -0000	1.14
@@ -3198,4 +3198,20 @@
 ################################################
 # AUTOMATE UPSTREAM FILE CREATION (2008-10-15 markd)
 update genbank.conf:
 panTro2.upstreamGeneTbl = refGene
+
+############################################################################
+# SWAP HG19 Chain/Net (DONE - 2009-04-25 - Hiram)
+    #	running the swap
+    ssh swarm
+    mkdir /hive/data/genomes/panTro2/bed/blastz.hg19.swap
+    cd /hive/data/genomes/panTro2/bed/blastz.hg19.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	-swap /hive/data/genomes/hg19/bed/lastzPanTro2.2009-03-19/DEF \
+	-noLoadChainSplit -chainMinScore=5000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=swarm -bigClusterHub=swarm \
+	> swap.log 2>&1 &
+    #	real    723m41.377s
+    cat fb.panTro2.chainHg19Link.txt 
+    #	2761343871 bases of 2909485072 (94.908%) in intersection
+############################################################################