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| author | Glenn P Johnson <glenn-johnson@uiowa.edu> | 2019-09-12 13:34:45 -0500 |
|---|---|---|
| committer | Peter Scheibel <scheibel1@llnl.gov> | 2019-09-13 19:08:57 -0700 |
| commit | 09047d76e9c84ad7c56c92f1de33cc272fcf9cb5 (patch) | |
| tree | f4a80b4b5ba8c0f178fb05c35bde6ec19edf78c7 /var | |
| parent | b046ee20f5ca0ff506967bd52029f4f9152b2ed8 (diff) | |
| download | spack-09047d76e9c84ad7c56c92f1de33cc272fcf9cb5.tar.gz spack-09047d76e9c84ad7c56c92f1de33cc272fcf9cb5.tar.bz2 spack-09047d76e9c84ad7c56c92f1de33cc272fcf9cb5.tar.xz spack-09047d76e9c84ad7c56c92f1de33cc272fcf9cb5.zip | |
Update braker package
- 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
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/braker/package.py | 39 |
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) |