src/hg/makeDb/doc/fr2.txt 1.24

Index: src/hg/makeDb/doc/fr2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/fr2.txt,v
retrieving revision 1.23
retrieving revision 1.24
diff -b -B -U 4 -r1.23 -r1.24
--- src/hg/makeDb/doc/fr2.txt	21 Jul 2009 21:01:42 -0000	1.23
+++ src/hg/makeDb/doc/fr2.txt	18 Sep 2009 22:15:32 -0000	1.24
@@ -1092,8 +1092,15 @@
 	multiz5way.mafFrames.gz
     #	real    0m20.580s
 
 #########################################################################
+# Adding automatic generation of upstream files (DONE - 2009-08-13 - Hiram)
+    # edit src/hg/makeDb/genbank/genbank.conf to add:
+
+fr2.upstreamGeneTbl = ensGene
+fr2.upstreamMaf = multiz5way /hive/data/genomes/fr2/bed/multiz5way/species.lst
+
+#########################################################################
 # MULTIZ5WAY DOWNLOADABLES (DONE - 2007-02-05 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/fr2/bed/multiz5way/mafDownloads
     cd /cluster/data/fr2/bed/multiz5way
@@ -1721,4 +1728,24 @@
    svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/usr/markd/svn/projs/transMap/tags/vertebrate.2009-07-01
 
 see doc/builds.txt for specific details.
 ############################################################################
+# LASTZ/CHAIN/NET fr2 (DONE - 2009-09-15,18 - Hiram)
+    # original alignment to tetNig2:
+    cd /hive/data/genomes/tetNig2/bed/lastzFr2.2009-09-15
+    cat fb.tetNig2.chainFr2Link.txt 
+    #	243965150 bases of 302314788 (80.699%) in intersection
+
+    #	and the swap to here, fr2:
+    mkdir /hive/data/genomes/fr2/bed/blastz.tetNig2.swap
+    cd /hive/data/genomes/fr2/bed/blastz.tetNig2.swap
+    time nice -n +19 doBlastzChainNet.pl -verbose=2 \
+	/hive/data/genomes/tetNig2/bed/lastzFr2.2009-09-15/DEF \
+	-swap -tRepeats=windowmaskerSdust \
+	-noLoadChainSplit -chainMinScore=2000 -chainLinearGap=medium \
+	-workhorse=hgwdev -smallClusterHub=memk -bigClusterHub=pk \
+	> swap.log 2>&1 &
+    #	real    21m56.576s
+    cat fb.fr2.chainTetNig2Link.txt 
+    #	248984008 bases of 393312790 (63.304%) in intersection
+
+#########################################################################