Generate Compara dumps for Plant Rectome (everything you need, I think)

dump_compara_orthologues.bash

## Get BioMart
git clone https://github.com/biomart/biomart-perl.git


## Get ready
cd biomart-perl/scripts


## Get Sharon's script from here:
## https://gist.github.com/dbolser-ebi/1890e35cb6d1366544e1346666cfe6f5
wget https://gist.githubusercontent.com/dbolser-ebi/1890e35cb6d1366544e1346666cfe6f5/raw/2b255a65db5b7ea3229cf938d0c6d7980a9b192f/biomart_perl_query_4Justin.pl


## Set up your Ensembl Perl environment
source /homes/dbolser/EG_Places/Devel/lib/libensembl-94/setup.sh


## I think I had to add XML parsing from cpan (using this handy guide:
## http://bioblog5000.blogspot.com/2011/12/this-way-individual-projects-with.html)
source local-lib.sh 


## Finally, add BioMart
export PERL5LIB=$PERL5LIB:$PWD/../lib 


## NOW EDIT ../conf/martURLLocation.xml !!!
## NOTE, MartService will create this for you!
## e.g.  http://ens-prod-1.ebi.ac.uk:10301/biomart/martservice?type=registry



## And we're more or less ready...

ensembl_version=$(perl -MBio::EnsEMBL::ApiVersion -e "print software_version")
eg_version=$(echo $ensembl_version-53 | bc)

echo $eg_version/$ensembl_version



## Note, run clean the first time (e.g. for testing), then cached
perl biomart_perl_query_4Justin.pl dcarota

db_list=~/Plants/Lists/plant_list-$eg_version.txt

while read -r db; do
    echo $db

    db=$(echo $db | perl -ne '
      die unless /^(\w)\w+_(\w+)_core_/; print "$1$2\n"
    ')

    time \
      perl ./biomart_perl_query_4Justin.pl \
	$db > Output/$db-$eg_version.out

    echo
done < \
    <(grep _core_ $db_list)


ls Output/*-$eg_version.out | wc -l 

tar -cjvf \
    compara_orthologues-$eg_version.tar.bz \
    Output/*-$eg_version.out

cp compara_orthologues-$eg_version.tar.bz \
    /nfs/panda/ensemblgenomes/ftp/pub/misc_data/gramene/

mail preecej@science.oregonstate.edu -S test < \
    <( echo ftp://ftp.ensemblgenomes.org/pub/misc_data/gramene/compara_orthologues-41.tar.bz )

Nice!