src/hg/makeDb/doc/sacCer2.txt 1.16

Index: src/hg/makeDb/doc/sacCer2.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/sacCer2.txt,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/hg/makeDb/doc/sacCer2.txt	14 Jan 2010 22:10:58 -0000	1.15
+++ src/hg/makeDb/doc/sacCer2.txt	2 Feb 2010 18:56:32 -0000	1.16
@@ -441,8 +441,24 @@
     mkdir -p axtChain/run
     cd axtChain/run
     ls -d ../../sac??? | xargs -L 1 basename > species.list
     cut -f1 ../../../../../chrom.sizes > chrom.list
+    cat << '_EOF_' > chain.csh
+#!/bin/csh -ef
+set S = $1
+set C = $2
+set IN = ../../psl/${C}.${S}.psl.gz
+set OUT = ${S}/${C}.chain
+mkdir -p ${S}
+zcat ${IN} \
+| axtChain -psl -verbose=0  -minScore=1000 -linearGap=medium stdin \
+    /hive/data/genomes/sacCer2/sacCer2.2bit \
+    -faQ ../../${S} stdout \
+| chainAntiRepeat /hive/data/genomes/sacCer2/sacCer2.2bit \
+    ../../${S}.2bit stdin ${OUT}
+'_EOF_'
+    # << happy emacs
+    chmod +x chain.csh
 
     cat << '_EOF_' > template
 #LOOP
 chain.csh $(path1) $(path2) {check out line+ $(root1)/$(root2).chain}