diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 36 |
1 files changed, 23 insertions, 13 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 3b9cac0555..6424fcdc18 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -4,6 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * +import glob class Augustus(MakefilePackage): @@ -22,6 +23,7 @@ class Augustus(MakefilePackage): version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830', url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz') + depends_on('perl', type=('build', 'run')) depends_on('bamtools') depends_on('gsl') depends_on('boost') @@ -29,7 +31,6 @@ class Augustus(MakefilePackage): depends_on('htslib', when='@3.3.1:') depends_on('bcftools', when='@3.3.1:') depends_on('samtools', when='@3.3.1:') - depends_on('tabix', when='@3.3.1:') depends_on('curl', when='@3.3.1:') def edit(self, spec, prefix): @@ -64,19 +65,19 @@ class Augustus(MakefilePackage): with working_dir(join_path('auxprogs', 'bam2wig')): makefile = FileFilter('Makefile') # point tools to spack installations - bcftools = self.spec['bcftools'].prefix.include - samtools = self.spec['samtools'].prefix.include - htslib = self.spec['htslib'].prefix.include - tabix = self.spec['tabix'].prefix.include + if 'bcftools' in spec: + bcftools = self.spec['bcftools'].prefix.include + makefile.filter('BCFTOOLS=.*$', + 'BCFTOOLS=%s' % bcftools) + if 'samtools' in spec: + samtools = self.spec['samtools'].prefix.include + makefile.filter('SAMTOOLS=.*$', + 'SAMTOOLS=%s' % samtools) + if 'htslib' in spec: + htslib = self.spec['htslib'].prefix.include + makefile.filter('HTSLIB=.*$', + 'HTSLIB=%s' % htslib) - makefile.filter('SAMTOOLS=.*$', - 'SAMTOOLS=%s' % samtools) - makefile.filter('HTSLIB=.*$', - 'HTSLIB=%s' % htslib) - makefile.filter('BCFTOOLS=.*$', - 'BCFTOOLS=%s' % bcftools) - makefile.filter('TABIX=.*$', - 'TABIX=%s' % tabix) # fix bad linking dirs makefile.filter('$(SAMTOOLS)/libbam.a', '$(SAMTOOLS)/../lib/libbam.a', string=True) @@ -88,6 +89,15 @@ class Augustus(MakefilePackage): install_tree('config', join_path(self.spec.prefix, 'config')) install_tree('scripts', join_path(self.spec.prefix, 'scripts')) + @run_after('install') + def filter_sbang(self): + with working_dir(self.prefix.scripts): + 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.set('AUGUSTUS_CONFIG_PATH', join_path( self.prefix, 'config')) |