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authorsnehring <snehring@users.noreply.github.com>2021-12-24 06:42:30 -0600
committerGitHub <noreply@github.com>2021-12-24 13:42:30 +0100
commita3048438c33c16591d94bdc668a2bb1721c15937 (patch)
tree39227dce52b8d93428fbf039b228ce22916109fd
parent63317785522b067882428e3b6ae639660fcd188b (diff)
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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.py20
-rw-r--r--var/spack/repos/builtin/packages/lordec/package.py27
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)