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Commit 296e9aa3 authored by Studer Gabriel's avatar Studer Gabriel
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explicitely add perl to "add secondary structure" command

The shebang for addss.pl in hhsuite 3 changed from /usr/bin/env perl
to /usr/bin/perl. The latter always uses the interpreter at an absolute
location. In our HPC environment we load "modules" that adjust the user
path. If using /usr/bin/perl, those adjustements have no effect.
parent 9062f20b
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...@@ -596,9 +596,9 @@ class HHblits: ...@@ -596,9 +596,9 @@ class HHblits:
return a3m_file return a3m_file
# add secondary structure annotation # add secondary structure annotation
addss_cmd = "%s %s" % (os.path.join(self.hhsuite_root, addss_cmd = "perl %s %s" % (os.path.join(self.hhsuite_root,
'scripts/addss.pl'), 'scripts/addss.pl'),
a3m_file) a3m_file)
env = dict(os.environ) env = dict(os.environ)
env.update({'PERL5LIB' : os.path.join(self.hhsuite_root, 'scripts'), env.update({'PERL5LIB' : os.path.join(self.hhsuite_root, 'scripts'),
'HHLIB' : os.path.join(self.hhsuite_root), 'HHLIB' : os.path.join(self.hhsuite_root),
......
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