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lordec update and gatb-core (#28119)

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* lordec: version update to 0.9 adding gatb-core as dep

* gatb-core: adding new package gatb-core
This commit is contained in:
snehring 2021-12-24 06:42:30 -06:00 committed by GitHub
parent 6331778552
commit a3048438c3
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2 changed files with 44 additions and 3 deletions
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20
var/spack/repos/builtin/packages/gatb-core/package.py Normal file
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@ -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'

27
var/spack/repos/builtin/packages/lordec/package.py
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@ -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)