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iq-tree: add new version delete duplicate package (#44043)

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* iq-tree: add new version delete duplicate package
* Replace iqtree2 dependency
   orthofinder: replace iqtree2 with iq-tree@2
   py-phylophlan: replace iqtree2 with iq-tree@2
This commit is contained in:
snehring 2024-05-08 11:02:06 -05:00 committed by GitHub
parent 65d1ae083c
commit b4411cf2db
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GPG Key ID: B5690EEEBB952194
4 changed files with 5 additions and 45 deletions
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3
var/spack/repos/builtin/packages/iq-tree/package.py
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@ -16,6 +16,9 @@ class IqTree(CMakePackage):
license("GPL-2.0-or-later")
version(
"2.3.2", tag="v2.3.1", commit="60f1aa68646ab84cc96b55a7548707adde15f47a", submodules=True
)
version(
"2.3.1", tag="v2.3.1", commit="2914a2f7aac0a1a3c4fadde42c83e5dee315186d", submodules=True
)

43
var/spack/repos/builtin/packages/iqtree2/package.py
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@ -1,43 +0,0 @@
# Copyright 2013-2024 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.package import *
class Iqtree2(CMakePackage):
"""Efficient and versatile phylogenomic software by maximum likelihood"""
homepage = "http://www.iqtree.org"
url = "https://github.com/iqtree/iqtree2/archive/refs/tags/v2.1.2.tar.gz"
license("GPL-2.0-or-later")
version("2.2.2.7", sha256="407a1a56d352ba9c2152a1d708cd29db872a41c252fbdc7acd8e0de0da8af008")
version("2.2.2", sha256="2e9ce79427b140bca5f48b31fb098f394a21a7c5116bbbada1e3eabdd6efe982")
version("2.1.2", sha256="3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a")
variant("lsd2", default=False, description="Build with LSD2 support")
depends_on("boost", type="link")
depends_on("eigen", type="link")
depends_on("zlib-api", type="link")
resource(
name="lsd2-rsrc",
url="https://github.com/tothuhien/lsd2/archive/refs/tags/v.2.4.1.tar.gz",
sha256="3d0921c96edb8f30498dc8a27878a76d785516043fbede4a72eefd84b5955458",
destination="lsd2-rsrc",
when="+lsd2",
)
@run_before("cmake")
def expand_resource(self):
copy_tree(join_path("lsd2-rsrc", "*"), "lsd2")
def cmake_cargs(self):
args = [self.define_from_variant("USE_LSD2", variant="lsd2")]
return args

2
var/spack/repos/builtin/packages/orthofinder/package.py
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@ -54,7 +54,7 @@ class Orthofinder(Package):
depends_on("blast-plus", type="run", when="+blast")
depends_on("mmseqs2", type="run", when="+mmseqs2")
depends_on("muscle5", type="run", when="+muscle")
depends_on("iqtree2", type="run", when="+iqtree")
depends_on("iq-tree@2", type="run", when="+iqtree")
depends_on("raxml", type="run", when="+raxml")
depends_on("raxml-ng", type="run", when="+raxml-ng")

2
var/spack/repos/builtin/packages/py-phylophlan/package.py
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@ -34,5 +34,5 @@ class PyPhylophlan(PythonPackage):
depends_on("mafft@7.310:", type=("build", "run"))
depends_on("fasttree@2.1.8:", type=("build", "run"))
depends_on("raxml@8.2.10:", type=("build", "run"))
depends_on("iqtree2", type=("build", "run"))
depends_on("iq-tree@2", type=("build", "run"))
depends_on("mash", type=("build", "run"))