diff external_tools/darwin/lib/hh/scripts/HHPaths.pm @ 6:2277dd59b9f9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/external_tools/darwin/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 [e-mail]
+#     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;