src/hg/makeDb/doc/ailMel1.txt 1.3

1.3 2010/01/25 19:43:27 hiram
genbank done for ailMel1
Index: src/hg/makeDb/doc/ailMel1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ailMel1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/ailMel1.txt	26 Dec 2009 06:09:30 -0000	1.2
+++ src/hg/makeDb/doc/ailMel1.txt	25 Jan 2010 19:43:27 -0000	1.3
@@ -1,135 +1,185 @@
 # for emacs: -*- mode: sh; -*-
 
 #	$Id$
 
 # Panda sequence: http://panda.genomics.org.cn/page/panda/download.jsp
 #	Ailuropoda melanoleuca
 
 ##########################################################################
 # Download sequence (DONE - 2009-12-17 - Hiram)
     mkdir /hive/data/genomes/ailMel1
     cd /hive/data/genomes/ailMel1
     mkdir download
     cd download
 
 wget --timestamping \
 'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
 
 wget --timestamping \
 'ftp://public.genomics.org.cn/BGI/panda/genome_sequence/panda_contig100.mapping_scaffolds_nucmer.list.clean.tab.sort.gff.gz'
 
 wget --timestamping \
 'ftp://panda.genomics.org.cn/pub/panda/panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz'
 
 
     faCount panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz > faCount.txt
 
     grep "^scaff" faCount.txt | awk '{print $1}' > scaffold.list
 
     faSomeRecords panda.scafSeq.gapFilled.noMito.GeneScaffold.fa.gz \
 	scaffold.list stdout | gzip > scaffolds.fa.gz
 
     hgFakeAgp scaffolds.fa.gz stdout | sed -e "s/D/W/" > fake.agp
 
 ##########################################################################
 # Initial genome build (DONE - 2009-12-17 - Hiram)
     cd /hive/data/genomes/ailMel1
 
     cat << '_EOF_' > ailMel1.config.ra
 # Config parameters for makeGenomeDb.pl:
 db ailMel1
 clade mammal
 genomeCladePriority 19
 scientificName Ailuropoda melanoleuca
 commonName Panda
 assemblyDate Dec. 2009
 assemblyLabel BGI-Shenzhen AilMel 1.0 Dec. 2009
 orderKey 220
 mitoAcc NC_009492
 fastaFiles /hive/data/genomes/ailMel1/download/scaffolds.fa.gz
 agpFiles /hive/data/genomes/ailMel1/download/fake.agp
 # qualFiles none
 dbDbSpeciesDir panda
 taxId 9646
 
     makeGenomeDb.pl -stop=seq ailMel1.config.ra > seq.out 2>&1
     makeGenomeDb.pl -start=agp -stop=agp ailMel1.config.ra > agp.out 2>&1
     makeGenomeDb.pl -start=db -stop=db ailMel1.config.ra > db.out 2>&1
     makeGenomeDb.pl -start=dbDb -stop=dbDb ailMel1.config.ra > dbDb.out 2>&1
     makeGenomeDb.pl -start=trackDb -stop=trackDb ailMel1.config.ra > trackDb.out 2>&1
 
 ##########################################################################
 # running repeat masker (DONE - 2009-12-21 - Hiram)
     mkdir /hive/data/genomes/ailMel1/bed/repeatMasker
     cd /hive/data/genomes/ailMel1/bed/repeatMasker
     doRepeatMasker.pl -buildDir=`pwd` -noSplit -bigClusterHub=swarm \
 	-workhorse=hgwdev ailMel > do.log 2>&1
     cat faSize.rmsk.txt
 # 2279048486 bases (54196431 N's 2224852055 real 1356361826 upper
 #	868490229 lower) in 12195 sequences in 1 files
 # %38.11 masked total, %39.04 masked real
 
 ##########################################################################
 # running simple repeat (DONE - 2009-12-21 - Hiram)
     mkdir /hive/data/genomes/ailMel1/bed/simpleRepeat
     cd /hive/data/genomes/ailMel1/bed/simpleRepeat
     doSimpleRepeat.pl -buildDir=`pwd` -smallClusterHub=swarm \
 	-workhorse=hgwdev ailMel > do.log 2>&1
 
     cat fb.simpleRepeat 
 # 24968229 bases of 2225124764 (1.122%) in intersection
 
     twoBitMask ailMel1.rmsk.2bit \
 	-add bed/simpleRepeat/trfMask.bed ailMel1.2bit
     #	you can safely ignore the warning about fields >= 13
 
     twoBitToFa ailMel1.2bit stdout | faSize stdin > faSize.ailMel1.2bit.txt
     cat faSize.ailMel1.2bit.txt
 # 2279048486 bases (54196431 N's 2224852055 real 1355773543 upper
 #	869078512 lower) in 12195 sequences in 1 files
 # %38.13 masked total, %39.06 masked real
     rm /gbdb/ailMel1/ailMel1.2bit
     ln -s `pwd`/ailMel1.2bit /gbdb/ailMel1/ailMel1.2bit
 
 ##########################################################################
 #  BLATSERVERS ENTRY (DONE - 2009-12-23 - Hiram)
 #	After getting a blat server assigned by the Blat Server Gods,
     ssh hgwdev
 
     hgsql -e 'INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
 	VALUES ("ailMel1", "blat12", "17802", "1", "0"); \
 	INSERT INTO blatServers (db, host, port, isTrans, canPcr) \
 	VALUES ("ailMel1", "blat12", "17803", "0", "1");' \
 	    hgcentraltest
     #	test it with some sequence
 
 #########################################################################
 # MAKE 11.OOC FILES FOR BLAT (DONE - 2009-12-23 - Hiram)
     ssh kolossus
     # numerator is ailMel1 gapless bases as reported by faSize 
     # denominator is hg17 gapless bases as reported by featureBits,
     # 1024 is threshold used for human -repMatch:
     calc \( 2224852055 / 2897310462 \) \* 1024
 # ( 2224852055 / 2897310462 ) * 1024 = 786.332198
     # ==> use -repMatch=750 according to size scaled down from 1024 for human.
     #	and rounded down to nearest 50
     cd /hive/data/genomes/ailMel1
     blat ailMel1.2bit /dev/null /dev/null -tileSize=11 \
       -makeOoc=jkStuff/ailMel1.11.ooc -repMatch=750
     #	Wrote 25042 overused 11-mers to jkStuff/ailMel1.11.ooc
 
     mkdir /hive/data/staging/data/ailMel
     cp -p ailMel1.2bit chrom.sizes jkStuff/ailMel1.11.ooc \
 	/hive/data/staging/data/ailMel1
 
 
 #########################################################################
 # genbank run
-    time nice -n +19 bin/gbAlignStep -initial  ailMel1 &
+    ssh hgwdev
+    cd $HOME/kent/src/hg/makeDb/genbank
+    # edit etc/genbank.conf to add this section just after canFam2:
+# ailMel1 (panda)
+ailMel1.serverGenome = /hive/data/genomes/ailMel1/ailMel1.2bit
+ailMel1.clusterGenome = /scratch/data/ailMel1/ailMel1.2bit
+ailMel1.lift = no
+ailMel1.ooc = /scratch/data/ailMel1/ailMel1.11.ooc
+ailMel1.refseq.mrna.native.pslCDnaFilter  = ${ordered.refseq.mrna.native.pslCDnaFilter}
+ailMel1.refseq.mrna.xeno.pslCDnaFilter    = ${ordered.refseq.mrna.xeno.pslCDnaFilter}
+ailMel1.genbank.mrna.native.pslCDnaFilter = ${ordered.genbank.mrna.native.pslCDnaFilter}
+ailMel1.genbank.mrna.xeno.pslCDnaFilter   = ${ordered.genbank.mrna.xeno.pslCDnaFilter}
+ailMel1.genbank.est.native.pslCDnaFilter  = ${ordered.genbank.est.native.pslCDnaFilter}
+ailMel1.refseq.mrna.native.load = yes
+ailMel1.refseq.mrna.xeno.load = yes
+ailMel1.genbank.mrna.xeno.load = yes
+ailMel1.downloadDir = ailMel1
+ailMel1.perChromTables = no
+
+    # Edit src/lib/gbGenome.c to add new species.  With these four lines:
+# static char *ailMelNames[] = {"Ailuropoda melanoleuca", "Canis familiaris",
+#                                "Canis sp.", "Canis lupus familiaris",
+#                                "Canis lupus", NULL};
+#   ... later ...
+# {"ailMel", ailMelNames},
+
+    cvs ci -m "adding ailMel - Panda with Dog specifications" src/lib/gbGenome.c
+    make install-server
 
-    logFile: var/build/logs/2009.12.24-15:03:26.ailMel1.initalign.log
+    ssh genbank
+    screen  # control this business with a screen since it takes a while
+    cd /cluster/data/genbank
+    time nice -n +19 bin/gbAlignStep -initial  ailMel1 &
+    #	logFile: var/build/logs/2009.12.24-15:03:26.ailMel1.initalign.log
 
+    ssh hgwdev
+    cd /cluster/data/genbank
  nice ./bin/gbDbLoadStep -drop -initialLoad ailMel1 &
-[1] 10050
-[hiram@hgwdev /cluster/data/genbank] logFile: var/dbload/hgwdev/logs/2009.12.25-00:08:46.dbload.log
+    #	logFile: var/dbload/hgwdev/logs/2009.12.25-00:08:46.dbload.log
+
+    # enable daily alignment and update of hgwdev
+    cd ~/kent/src/hg/makeDb/genbank
+    cvsup
+    # add oryCun2 to:
+        etc/align.dbs
+        etc/hgwdev.dbs
+    cvs ci -m "Adding ailMel1 - Panda - Ailuropoda melanoleuca" \
+	etc/align.dbs etc/hgwdev.dbs
+    make etc-update
+    #	done - 2010-01-19 - Hiram
+
+############################################################################
+# reset position to RHO location as found from blat of hg19 RHO gene
+    hgsql -e \
+'update dbDb set defaultPos="scaffold329:558576-566855" where name="ailMel1";' \
+	hgcentraltest
 
+############################################################################