phylosiftrc

#
# configuration file for Phylosift
# this file can be edited to change the behavior of Phylosift
# and cause it to use something other than the default values for certain variables
# This can be used, for example, on a shared computing system to store a single shared copy of the 
# phylosift database or programs.
#
# The system-wide config should be copied to $PREFIX/etc/phylosiftrc, e.g. /usr/local/etc/phylosiftrc
# User-specific config files can be copied to $HOME/.phylosiftrc, e.g. /home/koadman/.phylosiftrc
# User-specific configs override values in the system-wide config.
#
#
# paths to directories containing various required programs
# leave these blank to use whatever is found in $PATH
# $hmmer3_path="";
# $blast_path="";
# $pplacer_path="";
# $ps_path="";


# Direct paths to executables
#
# $pplacer       = "";
# $guppy         = "";
# $rppr          = "";
# $taxit         = "";
# $hmmalign      = "";
# $hmmbuild      = "";
# $raxml         = "";
# $readconciler  = "";
# $cmalign       = "";
# $pda           = "";
# $fasttree      = "";
# $lastdb        = "";
# $lastal        = "";
# $segment_tree  = "";

# paths to required datasets
# leave these blank to use whatever is in $prefix/share/phylosift
#
# $marker_path="";
# $ncbi_path="";
# $marker_dir="";
# $markers_extended_dir="";
# $ncbi_dir = "";
$marker_base_url = "http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers";
$ncbi_url = "http://edhar.genomecenter.ucdavis.edu/~koadman/ncbi.tgz";


# default settings for Phylosift behavior
#
# Command line
#
#$force    = 1;       #overrides a previous run otherwise stop
#$file_dir = ""; #Directory for output
#$paired   = 1;    # used for paired fastQ input split in 2 different files OR interleaved
#$custom = ""; #need a file containing the marker names to use without extensions ** marker names shouldn't contain '_'
#$continue = 0; #when a mode different than all is used, continue the rest of Phylosift after the section specified by the mode is finished
#$threads = 1;    #allows PS to use the number of threads specified
#$simple  = 0; # generate only a simple text taxonomic summary, no krona, no taxon names in jplace
#$isolate  = 0;    #use when processing one or more isolate genomes
#$besthit  = 0;    #should we keep only the best hit when there are multiple?
#$coverage = 0;    #provides a contig/scaffold coverage file
#$updated  = 1;    #Indicates if Phylosift uses the updated versions of the Markers.
#$marker_url    = undef;    # an alternate address to retrieve markers from
#$extended      = 0;        #Should the full extended set of markers be used?
#$remove_dup    = 1;        #removes duplicate taxons when using build_marker
#$keep_search   = 0; #prevents the files from the bastDir from being deleted after each chunk has completed
#$start_chunk          = 1;       #sets the chunk to start with
#$chunks               = undef;   #sets the number of chunks to be run
#$my_debug   = 0;          #print debugging messages?
#$disable_update_check=1; # can be used to disable the marker update check and download at startup

#
#FastSearch default parameters
#
#$CHUNK_MAX_SEQS = 20000;
#$CHUNK_MAX_SIZE = 10000000;
#$quality_threshold = 20;

#lastal parameters
#$lastal_evalue = "-e75";
#$lastal_long_evalue = "-e150";

#lastal rna parameters
#$lastal_rna_evalue = "-e75";
#$lastal_long_rna_evalue = "-e150";

#input sequence length parameters
#$lastal_short_seq_length = 500;
#$lastal_long_seq_length = 1000;

#hit parsing parameters
#$max_hit_overlap = 10;
#$best_hits_bit_score_range = 30; # all hits with a bit score within this amount of the best will be used
$align_fraction = 0.5; # at least this amount of min[length(query),length(marker)] must align to be considered a hit
$align_fraction_isolate = 0.8; # use this align_fraction when in isolate mode on long sequences

#
# MarkerAlign default parameters
#
#$min_aligned_residues=50;
#$rna_split_size = 500; #sequences longer than this value will undergo the long sequence pipeline
#$gap_character = "-";

#hmmalign

#cmalign
#$cm_align_long_tau = "1e-6";
#$cm_align_long_mxsize = "2500";
#$cm_align_long_ali = "";
#$cm_align_short_tau = "1e-20";
#$cm_align_short_mxsize = "2500";
#$cm_align_short_ali = "-l";

#
# pplacer.pm
#
#$pplacer_groups = 15;
#$pplacer_verbosity = 0;
#$max_submarker_dist = 0.15;
#$min_submarker_prob = 0.35;

#
# Summarize
#
#$krona_threshold = 0.01;


#
# UpdateDB
#
#$MAX_SGE_JOBS = 5000;
#$WORKDIR_normal = "/state/partition1/koadman/phylosift/";
#$WORKDIR_fatnode = "/data/scratch/koadman/phylosift/";
#$repository = "";
#$destination = "";
#$taxon_knockouts = "";
#$local_storage = "";
#$base_markers = "";