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-rw-r--r--var/spack/repos/builtin/packages/braker/package.py39
1 files changed, 33 insertions, 6 deletions
diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py
index 77ae5cfa59..e141eaebed 100644
--- a/var/spack/repos/builtin/packages/braker/package.py
+++ b/var/spack/repos/builtin/packages/braker/package.py
@@ -4,6 +4,8 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
+import os
+import glob
class Braker(Package):
@@ -11,9 +13,10 @@ class Braker(Package):
that combines the advantages of GeneMark-ET and AUGUSTUS"""
homepage = "http://exon.gatech.edu/braker1.html"
- url = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
+ url = "https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.4.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
+ version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52')
version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
@@ -22,7 +25,12 @@ class Braker(Package):
depends_on('perl-scalar-util-numeric', type=('build', 'run'))
depends_on('perl-parallel-forkmanager', type=('build', 'run'))
depends_on('perl-file-which', type=('build', 'run'))
- depends_on('augustus@3.2.3')
+ 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-file-homedir', when='@2.1.4:', type=('build', 'run'))
+ depends_on('augustus')
+ depends_on('augustus@3.2.3', when='@:2.1.0')
depends_on('genemark-et')
depends_on('bamtools')
depends_on('samtools')
@@ -30,10 +38,29 @@ class Braker(Package):
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
- install('braker.pl', prefix.bin)
- install('filterGenemark.pl', prefix.bin)
- install('filterIntronsFindStrand.pl', prefix.bin)
- install('helpMod.pm', prefix.lib)
+ if self.version < Version('2.1.2'):
+ install('braker.pl', prefix.bin)
+ install('filterGenemark.pl', prefix.bin)
+ install('filterIntronsFindStrand.pl', prefix.bin)
+ install('helpMod.pm', prefix.lib)
+ else:
+ install_tree('docs', prefix.docs)
+ install_tree('example', prefix.example)
+ with working_dir('scripts'):
+ install('helpMod.pm', prefix.lib)
+ files = glob.iglob('*.pl')
+ for file in files:
+ if os.path.isfile(file):
+ install(file, prefix.bin)
+
+ @run_after('install')
+ def filter_sbang(self):
+ with working_dir(self.prefix.bin):
+ pattern = '^#!.*/usr/bin/env 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)