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| author | snehring <7978778+snehring@users.noreply.github.com> | 2024-05-08 11:02:06 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2024-05-08 09:02:06 -0700 |
| commit | b4411cf2db1e1d5a8153e1e2f0108a65ffdcd9a1 (patch) | |
| tree | 8ab8ebc568b262812447a05db7d5b9761af78fa3 /var | |
| parent | 65d1ae083c2344ba45ca8c1b09790763323ac720 (diff) | |
| download | spack-b4411cf2db1e1d5a8153e1e2f0108a65ffdcd9a1.tar.gz spack-b4411cf2db1e1d5a8153e1e2f0108a65ffdcd9a1.tar.bz2 spack-b4411cf2db1e1d5a8153e1e2f0108a65ffdcd9a1.tar.xz spack-b4411cf2db1e1d5a8153e1e2f0108a65ffdcd9a1.zip | |
iq-tree: add new version delete duplicate package (#44043)
* 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
Diffstat (limited to 'var')
4 files changed, 5 insertions, 45 deletions
diff --git a/var/spack/repos/builtin/packages/iq-tree/package.py b/var/spack/repos/builtin/packages/iq-tree/package.py index ed40389985..981393d4a0 100644 --- a/var/spack/repos/builtin/packages/iq-tree/package.py +++ b/var/spack/repos/builtin/packages/iq-tree/package.py @@ -17,6 +17,9 @@ 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 ) version( diff --git a/var/spack/repos/builtin/packages/iqtree2/package.py b/var/spack/repos/builtin/packages/iqtree2/package.py deleted file mode 100644 index 36b28af74f..0000000000 --- a/var/spack/repos/builtin/packages/iqtree2/package.py +++ /dev/null @@ -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 diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py index c0e1b45cb1..df79d4e302 100644 --- a/var/spack/repos/builtin/packages/orthofinder/package.py +++ b/var/spack/repos/builtin/packages/orthofinder/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/py-phylophlan/package.py b/var/spack/repos/builtin/packages/py-phylophlan/package.py index 648f4924a3..4c31ba94d9 100644 --- a/var/spack/repos/builtin/packages/py-phylophlan/package.py +++ b/var/spack/repos/builtin/packages/py-phylophlan/package.py @@ -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")) |