src/hg/makeDb/doc/gasAcu1.txt 1.40

Index: src/hg/makeDb/doc/gasAcu1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/gasAcu1.txt,v
retrieving revision 1.39
retrieving revision 1.40
diff -b -B -U 4 -r1.39 -r1.40
--- src/hg/makeDb/doc/gasAcu1.txt	24 Sep 2009 20:55:31 -0000	1.39
+++ src/hg/makeDb/doc/gasAcu1.txt	22 Dec 2009 19:56:42 -0000	1.40
@@ -2787,5 +2787,24 @@
 by a single Makefile. This is available from:
    svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-09-13
 
 see doc/builds.txt for specific details.
-############################################################################
+#########################################################################
+# LASTZ/CHAIN/NET swap danRer6 (DONE - 2009-12-21 - Galt)
+    # original alignment to danRer6
+    cd /hive/data/genomes/danRer6/bed/lastzMm9.2009-12-21
+    cat fb.danRer6.chainMm9Link.txt
+    #  147479454 bases of 1506896106 (9.787%) in intersection
+
+    #   running the swap - DONE - 2009-12-21
+    mkdir /hive/data/genomes/gasAcu1/bed/blastz.danRer6.swap
+    cd /hive/data/genomes/gasAcu1/bed/blastz.danRer6.swap
+    time nice +19 doBlastzChainNet.pl -verbose=2 \
+        /hive/data/genomes/danRer6/bed/lastzGasAcu1.2009-12-21/DEF \
+        -noLoadChainSplit -chainMinScore=5000 -chainLinearGap=loose \
+        -workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=swarm \
+        -swap >& swap.log &
+    cat fb.gasAcu1.chainDanRer6Link.txt
+    #  114451338 bases of 446627861 (25.626%) in intersection
+
+#######################################################################
+