From 6c4e0b1bf14476a9687b9de403b6002a90778ff0 Mon Sep 17 00:00:00 2001
From: Justin Stanley <molecuul@users.noreply.github.com>
Date: Tue, 9 Oct 2018 18:54:32 -0500
Subject: [PATCH] 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
---
.../builtin/packages/sspace-standard/package.py | 14 +++++++++++++-
1 file changed, 13 insertions(+), 1 deletion(-)
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)
--
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