src/hg/makeDb/doc/calJac3.txt 1.9

Index: src/hg/makeDb/doc/calJac3.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/calJac3.txt,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/makeDb/doc/calJac3.txt	28 Apr 2010 23:16:15 -0000	1.8
+++ src/hg/makeDb/doc/calJac3.txt	10 May 2010 16:27:46 -0000	1.9
@@ -2,9 +2,9 @@
 
 #	$Id$
 
 # Marmoset sequence: http://panda.genomics.org.cn/page/panda/download.jsp
-# ftp.ncbi.nlm.nih.gov:genbank/genomes/Eukaryotes/vertebrates_mammals/
+# ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/
 #	Callithrix_jacchus/Callithrix_jacchus-3.2
 #	Callithrix jacchus
 
 ##########################################################################
@@ -14,9 +14,9 @@
     mkdir genbank
     cd genbank
     wget --timestamping -r --cut-dirs=6 --level=0 -nH -x \
 	--no-remove-listing -np \
-"ftp://ftp.ncbi.nlm.nih.gov:/genbank/genomes/Eukaryotes/vertebrates_mammals/Callithrix_jacchus/Callithrix_jacchus-3.2/*"
+"ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Callithrix_jacchus/Callithrix_jacchus-3.2/*"
 
     mkdir ucscChr
     cd ucscChr
     #	fixup the accession names to become UCSC chrom names
@@ -1244,8 +1244,9 @@
 
     find ../splitMaf -type f | grep "/[0-9][0-9][0-9].maf" \
 	| xargs -L 1 basename | sort -u > chr.part.list
     gensub2 chr.part.list single template jobList
+    mkdir maf
     para -ram=8g create jobList
 
     #	put the split mafs back together into a single result
     head -q -n 1 maf/000.maf > calJac3.13way.maf