# build curated assembly from hub https://hgdownload.soe.ucsc.edu/hubs/GCF/014/621/545/GCF_014621545.1/hub.txt

hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCF/014/621/545/GCF_014621545.1/
rsyncUrl=rsync://hgdownload.soe.ucsc.edu/hubs/GCF/014/621/545/GCF_014621545.1/
id=GCF_014621545.1
ucscName=mpxvRivers
assName="Monkeypox virus genome assembly ASM1462154v1"
org="Monkeypox"
orderKey=22325
defaultPos=NC_063383.1:65,736-75,736
taxId=10244

hgsql "" -Ne "create database $ucscName"

mkdir /gbdb/$ucscName
mkdir /cluster/data/genomes/$ucscName
cd /cluster/data/genomes/$ucscName

wget $hubUrl/$id.2bit -O $ucscName.2bit
ln -s `pwd`/$ucscName.2bit /gbdb/$ucscName

mkdir hubs
ln -s /hive/data/genomes/$ucscName/hubs /gbdb/$ucscName/hubs

rsync -rav $rsyncUrl/bbi .
ln -s /hive/data/genomes/$ucscName/bbi /gbdb/$ucscName/bbi

rsync -rav $rsyncUrl/ixIxx .
ln -s /hive/data/genomes/$ucscName/ixIxx /gbdb/$ucscName/ixIxx

rsync -rav $rsyncUrl/$id.chromAlias.bb hubs/chromAlias.bb 
rsync -rav $rsyncUrl/groups.txt hubs/groups.txt

mkdir ~/kent/src/hg/makeDb/trackDb/virus/mpxvRivers
cd  ~/kent/src/hg/makeDb/trackDb/virus/mpxvRivers

 wget -q -O /dev/stdout "https://hgdownload.soe.ucsc.edu/hubs/GCF/014/621/545/GCF_014621545.1/hub.txt" | raToLines /dev/stdin /dev/stdout |  grep "^ *track"| linesToRa /dev/stdin /dev/stdout |  sed "s?searchTrix ?& /gbdb/$ucscName/?" | sed "s?bigDataUrl ?& /gbdb/$ucscName/?" > trackDb.ra 

echo "insert into dbDb values(\"$ucscName\", \"$assName\", \"hub:/gbdb/$ucscName/hubs\", \"$org\", \"$defaultPos\", 1, \"$orderKey\", \"$org\", \"$org\", \"/gbdb/$ucscName/html/description.html\", 0, 1, \"$org\", \"$taxId\");" > insertDbDb.txt

echo "insert into blatServers values(\"$ucscName\", \"dynablat-01\", 4040, 1, 0, 1);" > blatServer.txt
echo "insert into blatServers values(\"$ucscName\", \"dynablat-01\", 4040, 0, 1, 1);" >> blatServer.txt