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Update braker package

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- add version 2.1.4
- change url to github
- add perl dependencies
- new version has a new source layout
- filter shebang to use spack perl
This commit is contained in:
Glenn P Johnson 2019-09-12 13:34:45 -05:00 committed by Peter Scheibel
parent b046ee20f5
commit 09047d76e9
1 changed files with 33 additions and 6 deletions
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39
var/spack/repos/builtin/packages/braker/package.py
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@ -4,6 +4,8 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import * from spack import *
import os
import glob
class Braker(Package): class Braker(Package):
@ -11,9 +13,10 @@ class Braker(Package):
that combines the advantages of GeneMark-ET and AUGUSTUS""" that combines the advantages of GeneMark-ET and AUGUSTUS"""
homepage = "http://exon.gatech.edu/braker1.html" 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" list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
version('2.1.4', sha256='d48af5649cc879343046f9ddf180fe2c709b5810e0b78cf314bf298514d31d52')
version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56') version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
version('1.11', '297efe4cabdd239b710ac2c45d81f6a5', version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz') 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-scalar-util-numeric', type=('build', 'run'))
depends_on('perl-parallel-forkmanager', type=('build', 'run')) depends_on('perl-parallel-forkmanager', type=('build', 'run'))
depends_on('perl-file-which', 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('genemark-et')
depends_on('bamtools') depends_on('bamtools')
depends_on('samtools') depends_on('samtools')
@ -30,10 +38,29 @@ class Braker(Package):
def install(self, spec, prefix): def install(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
mkdirp(prefix.lib) mkdirp(prefix.lib)
install('braker.pl', prefix.bin) if self.version < Version('2.1.2'):
install('filterGenemark.pl', prefix.bin) install('braker.pl', prefix.bin)
install('filterIntronsFindStrand.pl', prefix.bin) install('filterGenemark.pl', prefix.bin)
install('helpMod.pm', prefix.lib) 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): def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix.lib) run_env.prepend_path('PERL5LIB', prefix.lib)