Mercurial > repos > hammock > hammock
comparison external_tools/darwin/lib/hh/scripts/HHPaths.pm @ 6:2277dd59b9f9 draft
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author | hammock |
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date | Wed, 01 Nov 2017 05:54:28 -0400 |
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1 # HHPaths.pm | |
2 | |
3 # HHsuite version 2.0.15 (June 2012) | |
4 # (C) J. Soeding, A. Hauser 2012 | |
5 | |
6 # This program is free software: you can redistribute it and/or modify | |
7 # it under the terms of the GNU General Public License as published by | |
8 # the Free Software Foundation, either version 3 of the License, or | |
9 # (at your option) any later version. | |
10 | |
11 # This program is distributed in the hope that it will be useful, | |
12 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
14 # GNU General Public License for more details. | |
15 | |
16 # You should have received a copy of the GNU General Public License | |
17 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
18 | |
19 # We are very grateful for bug reports! Please contact us at soeding@genzentrum.lmu.de | |
20 # HHsuite version 2.0 | |
21 | |
22 # PLEASE INSERT CORRECT PATHS AT POSITIONS INDICATED BY ... BELOW | |
23 # THE ENVIRONMENT VARIABLE HHLIB NEEDS TO BE SET TO YOUR LOCAL HH-SUITE DIRECTORY, | |
24 # AS DESCRIBED IN THE HH-SUITE USER GUIDE AND README FILE | |
25 | |
26 package HHPaths; | |
27 | |
28 # This block can stay unmodified | |
29 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS $VERSION); | |
30 use Exporter; | |
31 our $VERSION = "version 2.0.16 (January 2013)"; | |
32 our @ISA = qw(Exporter); | |
33 our @EXPORT = qw($VERSION $hhlib $hhdata $hhbin $hhscripts $execdir $datadir $ncbidir $dummydb $pdbdir $dsspdir $dssp $cs_lib $context_lib $v); | |
34 | |
35 ############################################################################################## | |
36 # PLEASE COMPLETE THE PATHS ... TO PSIPRED AND OLD-STYLE BLAST (NOT BLAST+) (NEEDED FOR PSIPRED) | |
37 #our $execdir = ".../psipred/bin"; # path to PSIPRED V2 binaries | |
38 #our $datadir = ".../psipred/data"; # path to PSIPRED V2 data files | |
39 #our $ncbidir = ".../blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl) | |
40 our $execdir = "/cluster/toolkit/production/bioprogs/psipred/bin"; # path to PSIPRED V2 binaries | |
41 our $datadir = "/cluster/toolkit/production/bioprogs/psipred/data"; # path to PSIPRED V2 data files | |
42 our $ncbidir = "/cluster/toolkit/production/bioprogs/blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl) | |
43 | |
44 ############################################################################################## | |
45 # PLEASE COMPLETE THE PATHS ... TO YOUR LOCAL PDB FILES, DSSP FILES ETC. | |
46 #our $pdbdir = ".../pdb/all"; # where are the pdb files? (pdb/divided directory will also work) | |
47 #our $dsspdir = ".../dssp/data"; # where are the dssp files? Used in addss.pl. | |
48 #our $dssp = ".../dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl. | |
49 our $pdbdir = "/cluster/databases/pdb/all"; # where are the pdb files? (pdb/divided directory will also work) | |
50 our $dsspdir = "/cluster/databases/dssp/data"; # where are the dssp files? Used in addss.pl | |
51 our $dssp = "/cluster/databases/dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl | |
52 ############################################################################################## | |
53 | |
54 # The lines below probably do not need to be changed | |
55 | |
56 # Setting paths for hh-suite perl scripts | |
57 our $hhlib = $ENV{"HHLIB"}; # main hh-suite directory | |
58 our $hhdata = $hhlib."/data"; # path to data directory for hhblits, example files | |
59 our $hhbin = $hhlib."/bin"; # path to cstranslate (path to hhsearch, hhblits etc. should be in environment variable PATH) | |
60 our $hhscripts= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.) | |
61 our $dummydb = $hhdata."/do_not_delete"; # Name of dummy blast db for PSIPRED (single sequence formatted with NCBI formatdb) | |
62 | |
63 # HHblits data files | |
64 our $cs_lib = "$hhdata/cs219.lib"; | |
65 our $context_lib = "$hhdata/context_data.lib"; | |
66 | |
67 # Add hh-suite scripts directory to search path | |
68 $ENV{"PATH"} = $hhscripts.":".$ENV{"PATH"}; # Add hh scripts directory to environment variable PATH | |
69 | |
70 ################################################################################################ | |
71 ### System command with return value parsed from output | |
72 ################################################################################################ | |
73 sub System() | |
74 { | |
75 if ($v>=2) {printf("\$ %s\n",$_[0]);} | |
76 system($_[0]); | |
77 if ($? == -1) { | |
78 die("\nError: failed to execute '$_[0]': $!\n\n"); | |
79 } elsif ($? != 0) { | |
80 printf("\nError: command '$_[0]' returned error code %d\n\n", $? >> 8); | |
81 return 1; | |
82 } | |
83 return $?; | |
84 } | |
85 | |
86 return 1; |