prfdb.conf.complex

base = "${PRFDB_HOME}"
add_to_path = "$(base)/work:$(base)/bin"
blastdb = "$(prefix)/blast"
queue_table = "queue"
do_nupack = 1             ## Run nupack on sequences?
do_pknots = 1            ## Run pknots on sequence?
do_boot = 1               ## Perform our faux bootstrap
do_hotknots = 1
do_overlap = 1            ## Check on overlapping orfs
seqlength = ['100','75','50']
nupack_nopairs_hack = 1   ## For the NCI systems I hacked nupack
arch_specific_exe = 0     ## Architecture specific executables (used for a pbs environment)
boot_iterations = 100
boot_mfe_algorithms = { pknots => \&RNAFolders::Pknots_Boot, nupack => \&RNAFolders::Nupack_Boot_NOPAIRS, hotknots => \&RNAFolders::Hotknots_Boot, }
boot_randomizers = { array => \&SeqMisc::ArrayShuffle, }
errorfile = "$(prefix)/prfdb.err"            ## Error file
logfile = "$(prefix)/prfdb.log"           ## Location of output file
nupack = "Fold.out.nopairs"
nupack_boot = "Fold.out.boot.nopairs"
index_species = ['streptococcus_pyogenes', 'saccharomyces_cerevisiae', 'homo_sapiens', 'mus_musculus', 'danio_rerio', 'bos_taurus','rattus_norvegicus','xenopus_tropicalis', 'xenopus_laevis', 'haloarcula_marismortui', 'escherichia_coli', 'gallus_gallus', 'saccharomyces_paradoxus', 'saccharomyces_bayanus', 'saccharomyces_castellii', 'saccharomyces_kluyveri', 'saccharomyces_kudriavzevii', 'saccharomyces_mikatae', 'schizosaccharomyces_pombe', 'kluyveromyces_polysporous', 'virus']
maintenance_skip_optimize = 1
maintenance_skip_zscore = 1
maintenance_skip_stats = 1
maintenance_skip_index = 1