Mercurial > repos > hammock > hammock
diff external_tools/linux/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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/external_tools/linux/lib/hh/scripts/HHPaths.pm Wed Nov 01 05:54:28 2017 -0400 @@ -0,0 +1,86 @@ +# 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); + +############################################################################################## +# 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"}; # main hh-suite directory +our $hhdata = $hhlib."/data"; # path to 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= $hhlib."/scripts"; # path to hh perl scripts (addss.pl, reformat.pl, hhblitsdb.pl etc.) +our $dummydb = $hhdata."/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;