Index: src/hg/makeDb/doc/otoGar1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/otoGar1.txt,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 1000000 -r1.9 -r1.10
--- src/hg/makeDb/doc/otoGar1.txt	21 Jul 2009 21:01:45 -0000	1.9
+++ src/hg/makeDb/doc/otoGar1.txt	20 Sep 2009 17:16:46 -0000	1.10
@@ -1,149 +1,158 @@
 #This is the first release of the low-coverage 1.5X assembly of the bushbaby
 #(Otolemur garnettii). The genome sequencing and assembly is provided by the
 #Broad Institute.
 #
 #The N50 size is the length such that 50% of the assembled genome lies in
 #blocks of the N50 size or longer. The N50 length for supercontigs is 101.35 kb
 #and is 3.13 kb for contigs. The total number of bases in supercontigs is 3.39
 #Gb and in contigs is 1.97 Gb.
 #
 ##########################################################################
 #  Run the makeGenomeDb.pl script (DONE - 2006-12-18 - Robert)
     # prepare for the makeGenomeDb.pl script:
     ssh hgwdev
     cd /cluster/data/otoGar1
 cat << '_EOF_' > otoGar1.config.ra 
 # Config parameters for makeGenomeDb.pl:
 db otoGar1
 clade vertebrate
 genomeCladePriority 16
 commonName Bushbaby
 scientificName Otolemur garnetti 
 assemblyDate Dec. 2006
 assemblyLabel Broad version 1
 orderKey 16
 fakeAgpMinContigGap 25
 fakeAgpMinScaffoldGap 25 
 mitoAcc none
 fastaFiles /cluster/data/otoGar1/fromBroad/Draft_v1.agp.chromosome.fasta
 dbDbSpeciesDir bushbaby
 _EOF_
 
 ~/kent/src/hg/utils/automation/makeGenomeDb.pl otoGar1.config.ra
 ~/kent/src/hg/utils/automation/makeGenomeDb.pl otoGar1.config.ra -continue agp
 #########################################################################
 #WindowMasker
 ssh kolossus
 cd /cluster/data/otoGar1/bed
 ~/kent/src/hg/utils/automation/doWindowMasker.pl otoGar1 -workhorse=kolossus > wmRun.log 2>&1 &
 ssh hgwdev
 cd /cluster/data/otoGar1/bed/WindowMasker.2006-12-18/
 hgLoadBed otoGar1 windowmasker windowmasker.bed.gz
 
 #########################################################################
 # SIMPLE REPEATS (TRF) (DONE 2006-12-19 - Robert)
     ssh kolossus
     mkdir /cluster/data/otoGar1/bed/simpleRepeat
     cd /cluster/data/otoGar1/bed/simpleRepeat
     nice -n 19 time twoBitToFa ../../otoGar1.unmasked.2bit stdout \
 	| trfBig -trf=/cluster/bin/i386/trf stdin /dev/null \
 	    -bedAt=simpleRepeat.bed -tempDir=/tmp > trf.log 2>&1 &
     # Make a filtered version for sequence masking:
     awk '{if ($5 <= 12) print;}' simpleRepeat.bed > trfMask.bed
     splitFileByColumn trfMask.bed trfMaskChrom
 
     # Load unfiltered repeats into the database:
     ssh hgwdev
     hgLoadBed otoGar1 simpleRepeat \
       /cluster/data/otoGar1/bed/simpleRepeat/simpleRepeat.bed \
       -sqlTable=$HOME/kent/src/hg/lib/simpleRepeat.sql
     featureBits otoGar1 simpleRepeat
 
 #########################################################################
 # Mask seeds with orrb to do better alignments - Robert
 download and compile orrb from www.drive5.com/orrb  and copy to
 /cluster/bin/i386/orrb
 mkdir /cluster/data/otoGar1/orrb
 cd /cluster/data/otoGar1/orrb
 twoBitToFa ../otoGar1/otoGar1.unmasked.2bit \
    /san/sanvol1/scratch/otoGar/otoGar1.fa
 /cluster/bin/i386/orrb -mask /san/sanvol1/scratch/otoGar/otoGar1.fa \
                      -target /san/sanvol1/scratch/otoGar/otoGar1.fa\
                    -out otoGar1.maskOrrb.fa -wordsize 11 -threshalpha 13 \
                    -pattern 00011111000
 
 #########################################################################
 ## Processing photograph (DONE - 2007-02-15 - Hiram)
     ssh hgwdev
     mkdir /cluster/data/otoGar1/photograph
     cd /cluster/data/otoGar1/photograph
     cp -p /usr/local/apache/htdocs/images/Bu* ./BushBaby.jpg
     convert -quality 80 -normalize -sharpen 0 -geometry 200x320 BushBaby.jpg \
 	Otolemur_garnettii.jpg
     # add Otolemur_garnettii.jpg to the browser doc source tree and copy
     #	to /usr/local/apache/htdocs/images
     #	It is still a bit dark, a -gamma argument could lighten it
 
 ################################################
 # DOWNLOADS (2007-06-05 kate)
 
     ssh kkstore05
     cd /cluster/data/otoGar1
     mkdir bigZips
     cd bigZips
     nice twoBitToFa ../otoGar1.2bit otoGar1.fa
     nice gzip otoGar1.fa 
     md5sum *.gz > md5sum.txt
 
     ssh hgwdev
     set d = /usr/local/apache/htdocs/goldenPath
     set bd = /cluster/data/otoGar1
     cp $d/sorAra1/bigZips/README.txt $bd/bigZips
     # EDIT
     mkdir -p $d/otoGar1/bigZips
     ln -s $bd/bigZips/{*.gz,md5sum.txt,README.txt} $d/otoGar1/bigZips
    
 ############################################################################
 ##  BLASTZ swap from mm9 alignments (2007-11-11 - markd)
     ssh hgwdev
     mkdir /cluster/data/otoGar1/bed/blastz.mm9.swap
     cd /cluster/data/otoGar1/bed/blastz.mm9.swap
     ln -s blastz.mm9.swap ../blastz.mm9
     /cluster/bin/scripts/doBlastzChainNet.pl \
         -swap /cluster/data/mm9/bed/blastz.otoGar1/DEF >& swap.out&
 
     # fb.otoGar1.chainMm9Link.txt:
     #   592429209 bases of 1969052059 (30.087%) in intersection
 
 ############################################################################
 # TRANSMAP vertebrate.2008-05-20 build  (2008-05-24 markd)
 
 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.2008-05-20
 
 see doc/builds.txt for specific details.
 ############################################################################
 ############################################################################
 # TRANSMAP vertebrate.2008-06-07 build  (2008-06-30 markd)
 
 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.2008-06-30
 
 see doc/builds.txt for specific details.
 
 ############################################################################
 # add NCBI identifiers to the dbDb (DONE - 2008-10-21 - Hiram)
     hgsql -e 'update dbDb set
 sourceName="Broad version 1 (NCBI project 16955, AAQR00000000)" where name="otoGar1";' hgcentraltest
 ###########################################################################
 ############################################################################
 # TRANSMAP vertebrate.2009-07-01 build  (2009-07-21 markd)
 
 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.2009-07-01
 
 see doc/builds.txt for specific details.
 ############################################################################
+############################################################################
+# TRANSMAP vertebrate.2009-09-13 build  (2009-09-20 markd)
+
+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
+
+see doc/builds.txt for specific details.
+############################################################################

