Do not construct path to perl command manually (#6927)
Instead, use spec['perl'].command.path.
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parent
589ea856a5
commit
df7876ab54
5 changed files with 8 additions and 10 deletions
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@ -55,12 +55,11 @@ def filter_sbang(self):
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# We have to do this after install because otherwise the install
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# target will try to rebuild the binaries (filter_file updates the
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# timestamps)
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perl = join_path(self.spec['perl'].prefix.bin, 'perl')
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# Revert sbang, so Spack's sbang hook can fix it up
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filter_file('^#! /usr/bin/env perl',
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'#! {0} -w'.format(perl),
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'{0}/autom4te'.format(self.prefix.bin),
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'#! {0} -w'.format(self.spec['perl'].command.path),
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self.prefix.bin.autom4te,
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backup=False)
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def _make_executable(self, name):
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@ -42,9 +42,8 @@ class Canu(MakefilePackage):
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def patch(self):
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# Use our perl, not whatever is in the environment
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perl = self.spec['perl'].prefix.bin.perl
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filter_file(r'^#!/usr/bin/env perl',
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'#!{0}'.format(perl),
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'#!{0}'.format(self.spec['perl'].command.path),
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'src/pipelines/canu.pl')
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def install(self, spec, prefix):
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@ -64,10 +64,11 @@ def patch(self):
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@run_before('install')
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def filter_sbang(self):
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# Filter sbang before install so Spack's sbang hook can fix it up
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perl = join_path(self.spec['perl'].prefix.bin, 'perl')
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files = ['perl/feedGnuplot'] + glob.glob('filters/*')
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filter_file('^#!/usr/bin/perl', '#!{0}'.format(perl), *files)
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filter_file('^#!/usr/bin/perl',
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'#!{0}'.format(self.spec['perl'].command.path),
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*files)
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def install(self, spec, prefix):
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if self.compiler.name not in self.supported_compilers:
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@ -63,7 +63,7 @@ def install(self, spec, prefix):
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# Repeatmasker? (Y/N)
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# Add a Search Engine: Done
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config_answers = ['\n', '%s\n' % self.spec['perl'].prefix.bin.perl,
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config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
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'%s\n' % self.stage.source_path,
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'%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
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'%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
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@ -55,8 +55,7 @@ def filter_sbang(self):
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with working_dir('src/perl'):
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match = '^#!/usr/bin/env perl'
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perl = join_path(self.spec['perl'].prefix.bin, 'perl')
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substitute = "#!{perl}".format(perl=perl)
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substitute = "#!{perl}".format(perl=self.spec['perl'].command.path)
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# tab-to-vcf added in 0.1.15
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files = ['fill-aa', 'fill-an-ac', 'fill-fs',
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'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
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