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| author | snehring <snehring@users.noreply.github.com> | 2021-12-24 06:42:30 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-12-24 13:42:30 +0100 |
| commit | a3048438c33c16591d94bdc668a2bb1721c15937 (patch) | |
| tree | 39227dce52b8d93428fbf039b228ce22916109fd | |
| parent | 63317785522b067882428e3b6ae639660fcd188b (diff) | |
| download | spack-a3048438c33c16591d94bdc668a2bb1721c15937.tar.gz spack-a3048438c33c16591d94bdc668a2bb1721c15937.tar.bz2 spack-a3048438c33c16591d94bdc668a2bb1721c15937.tar.xz spack-a3048438c33c16591d94bdc668a2bb1721c15937.zip | |
lordec update and gatb-core (#28119)
* lordec: version update to 0.9 adding gatb-core as dep
* gatb-core: adding new package gatb-core
| -rw-r--r-- | var/spack/repos/builtin/packages/gatb-core/package.py | 20 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/lordec/package.py | 27 |
2 files changed, 44 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/gatb-core/package.py b/var/spack/repos/builtin/packages/gatb-core/package.py new file mode 100644 index 0000000000..fb90b24983 --- /dev/null +++ b/var/spack/repos/builtin/packages/gatb-core/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class GatbCore(CMakePackage): + """GATB - The Genome Analysis Toolbox with de-Bruijn graph""" + + homepage = "https://gatb.inria.fr/software/gatb-core/" + git = "https://github.com/GATB/gatb-core.git" + + depends_on('cmake@3.1.0:', type='build') + + version('1.4.2', tag='v1.4.2') + version('1.4.1', tag='v1.4.1') + + root_cmakelists_dir = 'gatb-core' diff --git a/var/spack/repos/builtin/packages/lordec/package.py b/var/spack/repos/builtin/packages/lordec/package.py index 40596ef398..47137c3721 100644 --- a/var/spack/repos/builtin/packages/lordec/package.py +++ b/var/spack/repos/builtin/packages/lordec/package.py @@ -14,12 +14,33 @@ class Lordec(MakefilePackage): homepage = "http://www.atgc-montpellier.fr/lordec/" url = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz" + version('0.9', sha256='8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b') version('0.8', sha256='3894a7c57649a3545b598f92a48d55eda66d729ab51606b00470c50611b12823') - depends_on('boost') - depends_on('cmake@3.1.0:', type='build') + def url_for_version(self, version): + if version == Version('0.8'): + return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz" + if version == Version('0.9'): + return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/lordec-src_0.9.tar.bz2" + + depends_on('boost@1.48.0:1.64.0', type=['build', 'link']) + depends_on('gatb-core@1.4.1:', type=['build', 'link', 'run']) + depends_on('zlib', type=['build', 'link']) build_targets = ['clean', 'all'] + def edit(self, spec, prefix): + lbstr = 'AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no' + filter_file('^AUTOMATIC_LIBBOOST_LOCAL_INSTALL.*$', lbstr, 'Makefile') + filter_file('gatb_v.*gatb_core.hpp', '', 'Makefile') + def install(self, spec, prefix): - install_tree('.', prefix.bin) + mkdir(prefix.include) + install('*.h', prefix.include) + mkdir(prefix.bin) + binaries = ['lordec-correct', 'lordec-stat', 'lordec-trim', + 'lordec-trim-split', 'lordec-build-SR-graph'] + for binary in binaries: + install(binary, prefix.bin) + mkdir(prefix.tools) + install('lordec_sge_slurm_wrapper.sh', prefix.tools) |