/usr/share/hhsuite/scripts/HHPaths.pm is in hhsuite-data 2.0.16-1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 | # HHPaths.pm
# HHsuite version 2.0.15 (June 2012)
# (C) J. Soeding, A. Hauser 2012
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# We are very grateful for bug reports! Please contact us at soeding@genzentrum.lmu.de
# HHsuite version 2.0
# PLEASE INSERT CORRECT PATHS AT POSITIONS INDICATED BY ... BELOW
# THE ENVIRONMENT VARIABLE HHLIB NEEDS TO BE SET TO YOUR LOCAL HH-SUITE DIRECTORY,
# AS DESCRIBED IN THE HH-SUITE USER GUIDE AND README FILE
package HHPaths;
# This block can stay unmodified
use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION);
use Exporter;
our $VERSION = "version 2.0.16 (January 2013)";
our @ISA = qw(Exporter);
our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v);
push @EXPORT, qw($hhshare $hhbdata);
##############################################################################################
# PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED)
#our $execdir = ".../psipred/bin"; # path to PSIPRED V2 binaries
#our $datadir = ".../psipred/data"; # path to PSIPRED V2 data files
#our $ncbidir = ".../blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl)
our $execdir = "/cluster/toolkit/production/bioprogs/psipred/bin"; # path to PSIPRED V2 binaries
our $datadir = "/cluster/toolkit/production/bioprogs/psipred/data"; # path to PSIPRED V2 data files
our $ncbidir = "/cluster/toolkit/production/bioprogs/blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl)
##############################################################################################
# PLEASE COMPLETE THE PATHS ... TO YOUR LOCAL PDB FILES, DSSP FILES ETC.
#our $pdbdir = ".../pdb/all"; # where are the pdb files? (pdb/divided directory will also work)
#our $dsspdir = ".../dssp/data"; # where are the dssp files? Used in addss.pl.
#our $dssp = ".../dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl.
our $pdbdir = "/cluster/databases/pdb/all"; # where are the pdb files? (pdb/divided directory will also work)
our $dsspdir = "/cluster/databases/dssp/data"; # where are the dssp files? Used in addss.pl
our $dssp = "/cluster/databases/dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl
##############################################################################################
# The lines below probably do not need to be changed
# Setting paths for hh-suite perl scripts
our $hhlib = $ENV{"HHLIB"} || "/usr/lib/hhsuite"; # main hh-suite directory
our $hhshare = $ENV{"HHLIB"} || "/usr/share/hhsuite"; # main hh-suite directory
our $hhdata = $hhshare."/data"; # path to arch indep data directory for hhblits, example files
our $hhbdata = $hhlib."/data"; # path to arch dep data directory for hhblits, example files
our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH)
our $hhscripts= $hhshare."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.)
our $dummydb = $hhbdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb)
# HHblits data files
our $cs_lib = "$hhdata/cs219.lib";
our $context_lib = "$hhdata/context_data.lib";
# Add hh-suite scripts directory to search path
$ENV{"PATH"} = $hhscripts.":".$ENV{"PATH"}; # Add hh scripts directory to environment variable PATH
################################################################################################
### System command with return value parsed from output
################################################################################################
sub System()
{
if ($v>=2) {printf("\$ %s\n",$_[0]);}
system($_[0]);
if ($? == -1) {
die("\nError: failed to execute '$_[0]': $!\n\n");
} elsif ($? != 0) {
printf("\nError: command '$_[0]' returned error code %d\n\n", $? >> 8);
return 1;
}
return $?;
}
return 1;
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