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| author | Justin Stanley <molecuul@users.noreply.github.com> | 2018-10-09 18:54:32 -0500 |
|---|---|---|
| committer | Peter Scheibel <scheibel1@llnl.gov> | 2018-10-09 16:54:32 -0700 |
| commit | 6c4e0b1bf14476a9687b9de403b6002a90778ff0 (patch) | |
| tree | 271de97d478c37f3dd80fbcf996ea7f267c869e0 | |
| parent | ca0d9ae7f024806a93295af19ec37aa491cdaac0 (diff) | |
| download | spack-6c4e0b1bf14476a9687b9de403b6002a90778ff0.tar.gz spack-6c4e0b1bf14476a9687b9de403b6002a90778ff0.tar.bz2 spack-6c4e0b1bf14476a9687b9de403b6002a90778ff0.tar.xz spack-6c4e0b1bf14476a9687b9de403b6002a90778ff0.zip | |
sspace-standard: add perl-perl4-corelibs dep, fix perl scripts (#9473)
perl scripts were pointing to /usr/bin/perl, changed to point to
the spack-installed perl
| -rw-r--r-- | var/spack/repos/builtin/packages/sspace-standard/package.py | 14 |
1 files changed, 13 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py index b1bba3273e..bf7f6a0679 100644 --- a/var/spack/repos/builtin/packages/sspace-standard/package.py +++ b/var/spack/repos/builtin/packages/sspace-standard/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * import os +import glob class SspaceStandard(Package): @@ -42,14 +43,25 @@ class SspaceStandard(Package): version('3.0', '7e171b4861b9d514e80aafc3d9cdf554') depends_on('perl+threads', type=('build', 'run')) + depends_on('perl-perl4-corelibs', type=('build', 'run')) 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('bowtie', prefix.bowtie) install_tree('bwa', prefix.bwa) install_tree('dotlib', prefix.dotlib) 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): run_env.set('SSPACE_HOME', prefix) |