phylosiftrc

# PhyloSift run control file
#
# see also:
# https://phylosift.wordpress.com/tutorials/running-phylosift/phylosift-run-control-file/
#

use Env qw($OMICS_REFERENCE_DATA);

my $common = "data9/flux/reference-data/phylosift";
my @ref_alternatives = (
    "$OMICS_REFERENCE_DATA/phylosift",
    "/geomicro/$common",
    "/gmb/$common",
    "/dept/geology/geomicro/$common",
);

foreach (@ref_alternatives) {
    $ref_data_path = $_ if (-d $_);
}
print "[phylosiftrc] using reference data from: $ref_data_path\n";

$marker_path = "$ref_data_path";
$ncbi_path = "$ref_data_path";

# prevent this:
#     Error: requested HMM banded DP mx of 4749.29 Mb > 2500.00 Mb limit.
#     Increase limit with --mxsize or tau with --tau.
$cm_align_long_mxsize = "10000";
$cm_align_short_mxsize = "10000";

# Use last-align bundled binaries if available

$lastdb        = "/usr/lib/phylosift/lastdb";
$lastal        = "/usr/lib/phylosift/lastal";

-e $lastdb or $lastdb="";
-e $lastal or $lastal="";