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| author | Aronnax, Miles V. [ISU/LAS] <rassilon@iastate.edu> | 2018-09-28 14:45:54 -0500 |
|---|---|---|
| committer | Levi Baber <baberlevi@gmail.com> | 2018-09-28 14:45:54 -0500 |
| commit | e9863f56f3335c37e342556f6758f1439226fa1d (patch) | |
| tree | 93f587b13cf7d5319d525afcafc8e9a7f7fa1b55 | |
| parent | d6daa8fab5ff64006c281d31a7a3996e2697cb77 (diff) | |
| download | spack-e9863f56f3335c37e342556f6758f1439226fa1d.tar.gz spack-e9863f56f3335c37e342556f6758f1439226fa1d.tar.bz2 spack-e9863f56f3335c37e342556f6758f1439226fa1d.tar.xz spack-e9863f56f3335c37e342556f6758f1439226fa1d.zip | |
Gapfiller 1.10 f01 (#9163)
* GapFiller.pl fixes: line endings, env perl, convert to Getopt::Std, requires perl with threads.
* GapFiller.pl fixed source path, install location.
* Fixed missing space.
| -rw-r--r-- | var/spack/repos/builtin/packages/gapfiller/package.py | 20 |
1 files changed, 16 insertions, 4 deletions
diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py index dc4e9ac9c8..35f8b106c8 100644 --- a/var/spack/repos/builtin/packages/gapfiller/package.py +++ b/var/spack/repos/builtin/packages/gapfiller/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * import os +import glob class Gapfiller(Package): @@ -44,9 +45,20 @@ class Gapfiller(Package): return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format( os.getcwd(), version.dashed) - depends_on('perl', type=('build', 'run')) + depends_on('perl+threads', type=('build', 'run')) + + def patch(self): + with working_dir('.'): + files = glob.iglob("*.pl") + for file in files: + change = FileFilter(file) + change.filter('usr/bin/perl', 'usr/bin/env perl') + change.filter('require "getopts.pl";', 'use Getopt::Std;') + change.filter('&Getopts', 'getopts') + change.filter('\r', '') + set_executable(file) def install(self, spec, prefix): - install_tree('bowtie', prefix.bowtie) - install_tree('bwa', prefix.bwa) - install('GapFiller.pl', prefix) + install_tree('bowtie', prefix.bin.bowtie) + install_tree('bwa', prefix.bin.bwa) + install('GapFiller.pl', prefix.bin) |