###
# Plasmodium falciparum 3D7 Version 12 from PlasmoDb  
# 2014-11-19:  markd
# This is a temporary genome build for a research project, it may eventually
# go to Todd's browser when he has the resources.  This will not be pushed
# public to the RR.
###
     cd /hive/data/genomes/plasFalc3D7V12

     # download fastas
     cd data/
     wget -nv     http://plasmodb.org/common/downloads/release-12.0/Pfalciparum3D7/fasta/data/PlasmoDB-12.0_Pfalciparum3D7_Genome.fasta

     # create plasFalc3D7V12.config.ra from one of the templates

     # download http://upload.wikimedia.org/wikipedia/commons/f/f1/Malaria.jpg and 
     # add to tree as htdocs/images/Plasmodium_falciparum_3D7.jpg

     makeGenomeDb.pl plasFalc3D7V12.config.ra >&make1.log

     # failed with: mustOpenFd: Can't open ./joinedRmskComposite.ra to read
     cp -r ~/compbio/browser/dev/kent/src/hg/makeDb/trackDb/joinedRmsk* TemporaryTrackDbCheckout/kent/src/hg/makeDb/trackDb/

     makeGenomeDb.pl -continue=trackDb plasFalc3D7V12.config.ra >&make2.log

     # update defaultDb
     update defaultDb set name="plasFalc3D7V12"  where genome ="Plasmodium falciparum 3D7";

     mkdir bed/genes
     (cd bed/genes && wget -nv    http://plasmodb.org/common/downloads/release-12.0/Pfalciparum3D7/gff/data/PlasmoDB-12.0_Pfalciparum3D7.gff)
     gff3ToGenePred bed/genes/PlasmoDB-12.0_Pfalciparum3D7.gff bed/genes/genes.gp
     hgLoadGenePred -genePredExt plasFalc3D7V12 genes bed/genes/genes.gp

     # link in 2bit.  We don't have a masked on currently
     ln -s /hive/data/genomes/plasFalc3D7V12/plasFalc3D7V12.unmasked.2bit /gbdb/plasFalc3D7V12/plasFalc3D7V12.2bit