src/hg/makeDb/doc/danRer6.txt 1.16

Index: src/hg/makeDb/doc/danRer6.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/danRer6.txt,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/hg/makeDb/doc/danRer6.txt	23 Dec 2009 19:02:44 -0000	1.15
+++ src/hg/makeDb/doc/danRer6.txt	26 Jan 2010 23:54:07 -0000	1.16
@@ -1020,5 +1020,25 @@
 vertebrate-wide transMap alignments were built  Tracks are created and loaded
 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
 
+
+##########################################################################
+# MAKE PER-CHROM FASTA DOWNLOADS (DONE 2010-01-25 galt)
+    ssh hgwdev
+    mkdir /cluster/data/danRer6/goldenPath/chromosomes
+    cd /cluster/data/danRer6/goldenPath/chromosomes
+    awk '$1 !~ /^chr/ {print $1;}' ../../chrom.sizes > scafs.lst
+    awk '$1 ~ /^chr/ {print $1;}' ../../chrom.sizes > chroms.lst
+    foreach chr (`cat chroms.lst`)
+      twoBitToFa ../../danRer6.2bit stdout -seq=$chr \
+      | gzip -c > $chr.fa.gz
+    end
+    twoBitToFa ../../danRer6.2bit stdout -seqList=scafs.lst \
+    | gzip -c > unmappedScaffolds.fa.gz
+    rm chroms.lst scafs.lst
+    md5sum *.gz > md5sum.txt
+    # Make README.txt
+    ln -s /cluster/data/danRer6/goldenPath/chromosomes \
+      /usr/local/apache/htdocs/goldenPath/danRer6/chromosomes
+
 ############################################################################