src/hg/makeDb/doc/ailMel1.txt 1.1
1.1 2009/12/23 22:54:57 hiram
Initial sequence for Panda
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 1.1
diff -b -B -U 4 -r1.2 -r1.1
--- src/hg/makeDb/doc/ailMel1.txt 26 Dec 2009 06:09:30 -0000 1.2
+++ src/hg/makeDb/doc/ailMel1.txt 23 Dec 2009 22:54:57 -0000 1.1
@@ -91,45 +91,4 @@
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 &
-
- logFile: var/build/logs/2009.12.24-15:03:26.ailMel1.initalign.log
-
- 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
-