#
# Configuration file for SAM/T2K.  This file is loaded by SamT2k.pm
# from the directory containing the executing script.  An alternate
# file can be specified with the SAM_T2K_CONF environment variable.
# Note: all variable references should be to the global space,
# ($::) as this is evaulated inside of a module.
#


# Machine architecture.
$::arch = `uname -m`;
chomp ($::arch);

# Path to blastp programs.  
$::wu_blast_prog = "/usr/local/bin/wu-blastp";
$::ncbi_blast_prog = "/usr/local/bin/blastall -p blastp";
$::ncbi_fastacmd_prog = "/usr/local/bin/fastacmd";

# Path to search for the GNU gunzip program.
$::gunzip_path = "/usr/local/bin:/usr/local/gnu/bin";

# Directory containing sam programs.
$::sam_bin_dir = "/usr/local/bin";

# Directory containing SAM-t2k programs
$::sam_t99_bin_dir = "/usr/local/bin";
$::sam_t2k_bin_dir = "/usr/local/bin";


# Where are regularizers kept?
$::reg_lib_dir = "/usr/local/lib/sam";

# Which non-redundant protein database to search.
$::NR = "/projects/compbio/data/nrp/nr";
    
# Where should temporary directory be built?
$::tmp_root_dir = "./tmp";

# Verbose output (logging of each external command executed)
$::verbose = 1;

# Standard Unix directory path.
$::unix_path = "/sbin:/usr/sbin:/bin:/usr/bin";

# Add program directories to path
$::ENV{"PATH"} = "$::sam_t2k_bin_dir:$::sam_bin_dir:$::gunzip_path:$::unix_path";

# Local Variables:
# mode: perl
# End:
