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