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sspace-standard: add perl-perl4-corelibs dep, fix perl scripts (#9473)

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perl scripts were pointing to /usr/bin/perl, changed to point to
the spack-installed perl
This commit is contained in:
Justin Stanley 2018-10-09 18:54:32 -05:00 committed by Peter Scheibel
parent ca0d9ae7f0
commit 6c4e0b1bf1
1 changed files with 13 additions and 1 deletions
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14
var/spack/repos/builtin/packages/sspace-standard/package.py
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@ -24,6 +24,7 @@
############################################################################## ##############################################################################
from spack import * from spack import *
import os import os
import glob
class SspaceStandard(Package): class SspaceStandard(Package):
@ -42,14 +43,25 @@ class SspaceStandard(Package):
version('3.0', '7e171b4861b9d514e80aafc3d9cdf554') version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
depends_on('perl+threads', type=('build', 'run')) depends_on('perl+threads', type=('build', 'run'))
depends_on('perl-perl4-corelibs', type=('build', 'run'))
def install(self, spec, prefix): def install(self, spec, prefix):
rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
scripts = [rootscript]
scripts.extend(glob.glob('tools/*.pl'))
scripts.extend(glob.glob('bwa/*.pl'))
for s in scripts:
filter_file('/usr/bin/perl', '/usr/bin/env perl',
s, string=True)
install_tree('bin', prefix.bin) install_tree('bin', prefix.bin)
install_tree('bowtie', prefix.bowtie) install_tree('bowtie', prefix.bowtie)
install_tree('bwa', prefix.bwa) install_tree('bwa', prefix.bwa)
install_tree('dotlib', prefix.dotlib) install_tree('dotlib', prefix.dotlib)
install_tree('tools', prefix.tools) install_tree('tools', prefix.tools)
install('SSPACE_Standard_v{0}.pl'.format(self.version), prefix) install(rootscript, prefix)
def setup_environment(self, spack_env, run_env): def setup_environment(self, spack_env, run_env):
run_env.set('SSPACE_HOME', prefix) run_env.set('SSPACE_HOME', prefix)