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repeatmasker: perl and HMMER dependency fixes (#11660)

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repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
This commit is contained in:
Justin S 2019-06-18 13:11:00 -05:00 committed by Peter Scheibel
parent e35355f040
commit d82f8cd405
1 changed files with 11 additions and 0 deletions
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11
var/spack/repos/builtin/packages/repeatmasker/package.py
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@ -4,6 +4,7 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import * from spack import *
import glob
class Repeatmasker(Package): class Repeatmasker(Package):
@ -71,6 +72,11 @@ def install(self, spec, prefix):
self.spec['ncbi-rmblastn'].prefix.bin, self.spec['ncbi-rmblastn'].prefix.bin,
'Y']) 'Y'])
# set non-default HMMER search
config_answers.extend(['3',
self.spec['hmmer'].prefix,
'N'])
# end configuration # end configuration
config_answers.append('5') config_answers.append('5')
@ -83,4 +89,9 @@ def install(self, spec, prefix):
perl = which('perl') perl = which('perl')
perl('configure', input=f) perl('configure', input=f)
# fix perl paths
# every sbang points to perl, so a regex will suffice
for f in glob.glob('*.pm'):
filter_file('#!.*', '#!%s' % spec['perl'].command, f)
install_tree('.', prefix.bin) install_tree('.', prefix.bin)