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| author | Glenn P Johnson <glenn-johnson@uiowa.edu> | 2019-09-12 09:49:54 -0500 |
|---|---|---|
| committer | Peter Scheibel <scheibel1@llnl.gov> | 2019-09-13 19:05:02 -0700 |
| commit | 2256890d4e86307cef3fa2abf7fa328432bcae7e (patch) | |
| tree | beecd405f57f0de2fdee3dcabed05cf105c12688 | |
| parent | 6df57bb2d0619a22b0bb0a5028b7caef7f31e722 (diff) | |
| download | spack-2256890d4e86307cef3fa2abf7fa328432bcae7e.tar.gz spack-2256890d4e86307cef3fa2abf7fa328432bcae7e.tar.bz2 spack-2256890d4e86307cef3fa2abf7fa328432bcae7e.tar.xz spack-2256890d4e86307cef3fa2abf7fa328432bcae7e.zip | |
Update genemark-et package
- add version 4.46
- add missing perl dependencies
- new version has different source layout
- filter shebang to use spack perl
| -rw-r--r-- | var/spack/repos/builtin/packages/genemark-et/package.py | 20 |
1 files changed, 19 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py index bb41a3e7ff..a25a942417 100644 --- a/var/spack/repos/builtin/packages/genemark-et/package.py +++ b/var/spack/repos/builtin/packages/genemark-et/package.py @@ -19,10 +19,15 @@ class GenemarkEt(Package): homepage = "http://topaz.gatech.edu/GeneMark" + version('4.46', sha256='856b0b6c7cbd12835e140ff04ecd9124376348efd65f76bfd8b8e08c1834eac0') version('4.38', sha256='cee3bd73d331be44159eac15469560d0b07ffa2c98ac764c37219e1f3b7d3146') version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3') depends_on('perl', type=('build', 'run')) + depends_on('perl-yaml', type=('build', 'run')) + depends_on('perl-hash-merge', type=('build', 'run')) + depends_on('perl-logger-simple', type=('build', 'run')) + depends_on('perl-parallel-forkmanager', type=('build', 'run')) def url_for_version(self, version): return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd()) @@ -30,7 +35,11 @@ class GenemarkEt(Package): def install(self, spec, prefix): mkdirp(prefix.bin) mkdirp(prefix.bin.heu_dir) - with working_dir('gmes_petap'): + if self.version <= Version('4.38'): + source_dir = 'gmes_petap' + else: + source_dir = self.stage.source_path + with working_dir(source_dir): install_tree('lib', prefix.lib) files = glob.iglob('*') for file in files: @@ -38,5 +47,14 @@ class GenemarkEt(Package): install(file, prefix.bin) install_tree('heu_dir', prefix.bin.heu_dir) + @run_after('install') + def filter_sbang(self): + with working_dir(self.prefix.bin): + pattern = '^#!.*/usr/bin/perl' + repl = '#!{0}'.format(self.spec['perl'].command.path) + files = glob.iglob("*.pl") + for file in files: + filter_file(pattern, repl, *files, backup=False) + def setup_environment(self, spack_env, run_env): run_env.prepend_path('PERL5LIB', prefix.lib) |