##V.1   do not remove this line
# MetaPathways v1.0 
# Kishori M. Konwar, Niels W. Hanson
# Parameter File

INPUT:format fasta
# e.g. fasta gbk-annotated gbk-unannotated gff-annotated gff-unannotated

# Quality Control  parameters 
quality_control:min_length 180
quality_control:delete_replicates yes

# ORF prediction parameters 
orf_prediction:algorithm prodigal
orf_prediction:min_length 60
orf_prediction:translation_table 11

# ORF annotation parameters
annotation:algorithm BLAST
# e.g. BLAST or LAST

#annotation:dbs metacyc-v4-2011-07-03,refseq-nr-2014-01-18,CAZY_2014_09_04,COG_2013-12-27,kegg-pep-2011-06-18,seed-2014-01-30
#annotation:dbs kegg-pep-2011-06-18,seed-2014-01-30
#annotation:dbs 
#annotation:dbs metacyc-v4-2011-07-03,refseq-nr-2014-01-18,CAZY_2014_09_04,COG_2013-12-27,kegg-pep-2011-06-18,seed-2014-01-30
annotation:dbs 

# e.g. annotation:dbs    cog,kegg,refseq,metacyc
annotation:min_bsr 0.4
annotation:max_evalue 0.000001
annotation:min_score 20
annotation:min_length 60
annotation:max_hits 10

# rRNA annotation parameters LSURef_115_tax_silva
rRNA:refdbs 

rRNA:max_evalue 0.000001
rRNA:min_identity 20
rRNA:min_bitscore 50

# pathway tools parameters
ptools_settings:taxonomic_pruning no

# grid settings

# pipeline execution flags
# e.g. yes, skip, yes
metapaths_steps:PREPROCESS_INPUT skip
metapaths_steps:ORF_PREDICTION skip
metapaths_steps:FILTER_AMINOS skip
metapaths_steps:FUNC_SEARCH skip
metapaths_steps:PARSE_FUNC_SEARCH skip
metapaths_steps:SCAN_rRNA skip
metapaths_steps:SCAN_tRNA skip
metapaths_steps:ANNOTATE_ORFS skip
metapaths_steps:GENBANK_FILE yes
metapaths_steps:BUILD_PGDB redo
metapaths_steps:COMPUTE_RPKM redo

# grid settings
# template for adding grid
# N is a digit, and should be unique for each grid
# note the settings below are commented out

#grid_engineN:server myserver
#grid_engineN:os linux
#grid_engineN:bit bit64
#grid_engineN:optional_string 
#grid_engineN:sshKey 
#grid_engineN:user who
#grid_engineN:max_parallel_jobs 3
#grid_engineN:name 



grid_engine0:server bugaboo.westgrid.ca
grid_engine0:os linux
grid_engine0:enabled no
grid_engine0:optional_string PBS -l walltime=10:00:00  -l pmem=10000mb
grid_engine0:bit bit64
grid_engine0:sshKey 
grid_engine0:user kishori
grid_engine0:max_parallel_jobs 3
grid_engine0:name 

grid_engine1:server orcinus.westgrid.ca
grid_engine1:os linux
grid_engine1:enabled yes
grid_engine1:optional_string PBS -l walltime=10:00:00  -l pmem=10000mb
grid_engine1:bit bit64
grid_engine1:sshKey 
grid_engine1:user kishori
grid_engine1:max_parallel_jobs 3
grid_engine1:name