src/hg/makeDb/doc/hg19.txt 1.104

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.103
retrieving revision 1.104
diff -b -B -U 4 -r1.103 -r1.104
--- src/hg/makeDb/doc/hg19.txt	21 Apr 2010 20:57:24 -0000	1.103
+++ src/hg/makeDb/doc/hg19.txt	30 Apr 2010 18:45:00 -0000	1.104
@@ -8572,9 +8572,11 @@
 # ENCODE Mapability track. 
 # 2010-02-05 Added a 40mer sequence subtrack received on 2010-02-04.
 # 2010-03-16 - 2010-03-18. Added metadata to trackDb for the subtracks and
 # added downloads for the bigWig data files.
-
+# 2010-04-28. Received new data from Thomas Derrien. Downloaded data and 
+# added it to /gbdb/. A bug was found in a library used by bedGraphToBigWig so
+# sent a new binary to data providers and they re-created the bigWig files. 
     mkdir -p /hive/data/genomes/hg19/bed/crgMapability
     cd /hive/data/genomes/hg19/bed/crgMapability
 cat << 'EOF' > temp
 #!/bin/tcsh -ef
@@ -8676,8 +8678,43 @@
      # Then run encodeDownloadsPages.pl
      /cluster/home/hartera/bin/encodeDownloadsPage.pl -db=hg19 -checksum \
           -preamble=preamble.html index.html . 
 
+     # Downloaded and added new bigWig files to /gbdb/hg19/bbi 
+     # (2010-04-28 and 2010-04-30, hartera). New files were created as 
+     # there was a bug in the older version of bedGraphToBigWig.          
+     cd /hive/data/genomes/hg19/bed/crgMapability
+     rm temp download.csh download.log 
+cat << 'EOF' > temp
+#!/bin/tcsh -ef
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-100.bw.bz2
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-24.bw.bz2
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-36.bw.bz2
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-40.bw.bz2
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-50.bw.bz2
+http://genome.crg.es/~tderrien/UCSC_Tracks/H.sapiens.genome.hg19.main.mappability-75.bw.bz2
+'EOF'
+     awk '{if ($0 ~ /#/) print; else print "wget --timestamping \"" $0 "\"";}' \
+         temp > download.csh
+     rm temp
+     chmod +x download.csh
+     ./download.csh >& download.log &
+
+     # Add data to /gbdb/. The file names in /gbdb/ are the same as before 
+     # so the tables do not need to be reloaded.
+     cd /hive/data/genomes/hg19/bed/crgMapability
+     bunzip2 *.bz2
+     foreach f (`ls *.bw`)
+       echo $f
+       set g=`echo $f | cut -d "-" -f2`
+       set num=`echo $g | cut -d "." -f1`
+       set mer=`echo "${num}mer"`
+       set nf=`echo "encCrgMapabilityAlign${mer}.bw"`
+       echo $nf
+       rm /gbdb/hg19/bbi/${nf}
+       ln -s `pwd`/${f} /gbdb/hg19/bbi/${nf}
+     end
+
 #####################################################################
 # tRNAs track (2010-01-13, Fan DONE)
 # tRNAs track (2010-03-10, Fan RE-BUILT WITH UPDATED DATA FROM TODD LOWE)
 #