run_maker_wq

#!/bin/bash

LOC="`pwd`"

INPUT=`echo *.fa*`

export PATH="$PATH:$LOC/maker/bin"
export PATH="$PATH:$LOC/external/bin"
export PATH="$PATH:$LOC/external/exe/blast/bin"
export PATH="$PATH:$LOC/external/exe/snap/bin"
export PATH="$PATH:$LOC/external/exe/repeatmasker"
export PATH="$PATH:$LOC/external/exe/exonerate/bin"
#export PATH="$PATH:$LOC/external/exe/augustus/bin"

export PERL5LIB="$LOC/maker/lib"
export PERL5LIB="$PERL5LIB:$LOC/maker/perl/lib"
export PERL5LIB="$PERL5LIB:$LOC/external/lib/perl5"
export PERL5LIB="$PERL5LIB:$LOC/external/lib/perl5/x86_64-linux-thread-multi"

export PERL5LIB="$PERL5LIB:$LOC/cctools/lib/perl5/site_perl/5.8.8/"

MAKER="perl `which maker_wq` -wq -d all"

#$MAKER -CTL
#sed -i "s/^genome=.*\$/genome=$INPUT/" maker_opts.ctl
#sed -i "s/^blast_type=.*$/blast_type=ncbi+/" maker_bopts.ctl

echo $MAKER $*
$MAKER $*

#rm *.ctl