src/hg/makeDb/doc/hg19.txt 1.43

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.42
retrieving revision 1.43
diff -b -B -U 4 -r1.42 -r1.43
--- src/hg/makeDb/doc/hg19.txt	1 Oct 2009 18:39:47 -0000	1.42
+++ src/hg/makeDb/doc/hg19.txt	13 Oct 2009 07:54:37 -0000	1.43
@@ -6384,8 +6384,61 @@
     hgLoadBed hg19 gnfAtlas2 gnfAtlas2.bed
     # Loaded 36357 elements of size 15
 
 ##########################################################################
+# BUILD NIBB IMAGE PROBES (DONE 2009-10-12 JK)
+
+# Make directory on san for cluster job and copy in sequence
+    ssh swarm
+    mkdir /hive/data/genomes/hg19/bed/nibbPics
+    cd /hive/data/genomes/hg19/bed/nibbPics
+    cp /cluster/data/xenTro1/bed/nibbPics/nibbImageProbes.fa .
+
+# Make parasol job dir and sequence list files
+    mkdir run
+    cd run
+    mkdir psl
+    ls -1 /scratch/data/hg19/nib/*.nib > genome.lst
+    echo ../nibbImageProbes.fa > mrna.lst
+
+# Create parasol gensub file file
+cat << '_EOF_' > gsub
+#LOOP
+blatz -rna -minScore=6000 -out=psl $(path1) $(path2) psl/$(root1)_$(root2).psl
+#ENDLOOP
+'_EOF_'
+
+# Create parasol batch
+    gensub2 genome.lst mrna.lst gsub spec
+    para create spec
+
+# Do para try/push/time etc.
+#Completed: 93 of 93 jobs
+#CPU time in finished jobs:       8008s     133.47m     2.22h    0.09d  0.000 y
+#IO & Wait Time:                   364s       6.07m     0.10h    0.00d  0.000 y
+#Average job time:                  90s       1.50m     0.03h    0.00d
+#Longest finished job:             765s      12.75m     0.21h    0.01d
+#Submission to last job:           824s      13.73m     0.23h    0.01d
+
+# Make sort and filter
+    catDir psl | sort -k 10 \
+        | pslReps stdin stdout /dev/null -nohead -minAli=0.60 -nearTop=0.001 -minCover=0.10 -minNearTopSize=80 \
+	| sort -k 14,14 -k 16,16n \
+	| sed 's#/scratch/data/hg19/nib/chr#chr#' \
+	| sed 's/.nib//' > ../nibbImageProbes.psl
+
+# Make bed file and copy in stuff
+    ssh hgwdev
+    cd /hive/data/genomes/hg19/bed/nibbPics
+    cp /cluster/data/xenTro1/bed/nibbPics/nibbImageProbes.fa .
+
+# Load into database
+    ln -s /cluster/data/hg19/bed/nibbPics/nibbImageProbes.fa /gbdb/hg19/nibbImageProbes.fa
+    hgLoadSeq hg19 /gbdb/hg19/nibbImageProbes.fa
+    hgLoadPsl hg19 nibbImageProbes.psl
+
+
+##########################################################################
 # make new grp table to match hg18 (DONE  2009-10-01 kuhn)
 # to split regulation from expression 
 # phenDis group is also missing in hg19
 # and add one more column: defaultIsClosed