diff options
6 files changed, 108 insertions, 15 deletions
diff --git a/var/spack/repos/builtin/packages/iqtree2/package.py b/var/spack/repos/builtin/packages/iqtree2/package.py new file mode 100644 index 0000000000..58a35eac72 --- /dev/null +++ b/var/spack/repos/builtin/packages/iqtree2/package.py @@ -0,0 +1,20 @@ +# Copyright 2013-2022 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" + + version("2.1.2", sha256="3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a") + + depends_on("boost", type="link") + depends_on("eigen", type="link") + depends_on("zlib", type="link") diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py index b79a9135dc..48ac925b1a 100644 --- a/var/spack/repos/builtin/packages/py-dendropy/package.py +++ b/var/spack/repos/builtin/packages/py-dendropy/package.py @@ -16,8 +16,9 @@ class PyDendropy(PythonPackage): homepage = "https://www.dendropy.org" pypi = "dendropy/DendroPy-4.3.0.tar.gz" + version("4.5.2", sha256="3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101") version("4.3.0", sha256="bd5b35ce1a1c9253209b7b5f3939ac22beaa70e787f8129149b4f7ffe865d510") version("3.12.0", sha256="38a0f36f2f7aae43ec5599408b0d0a4c80996b749589f025940d955a70fc82d4") - depends_on("python@2.7:,3.4:") - depends_on("py-setuptools", type="build") + depends_on("python@2.7:,3.4:", type=("build", "run")) + depends_on("py-setuptools", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-hclust2/package.py b/var/spack/repos/builtin/packages/py-hclust2/package.py new file mode 100644 index 0000000000..6968f13199 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hclust2/package.py @@ -0,0 +1,23 @@ +# Copyright 2013-2022 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 PyHclust2(PythonPackage): + """Hclust2 is a handy tool for plotting heat-maps with several useful + options to produce high quality figures that can be used in publication.""" + + homepage = "https://github.com/SegataLab/hclust2/" + pypi = "hclust2/hclust2-1.0.0.tar.gz" + + version("1.0.0", sha256="9667f1d16628940aedd3d1d571b956a6f77795018e3ea4dd83f234419eb0096d") + + depends_on("py-setuptools", type="build") + depends_on("py-numpy", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-metaphlan/package.py b/var/spack/repos/builtin/packages/py-metaphlan/package.py new file mode 100644 index 0000000000..5fcadcc527 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-metaphlan/package.py @@ -0,0 +1,40 @@ +# Copyright 2013-2022 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 PyMetaphlan(PythonPackage): + """MetaPhlAn is a computational tool for profiling the composition of + microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic + shotgun sequencing data (i.e. not 16S) with species-level.""" + + homepage = "https://github.com/biobakery/MetaPhlAn/" + pypi = "MetaPhlAn/MetaPhlAn-4.0.2.tar.gz" + + version("4.0.2", sha256="2549fdf2de97a0024551a7bb8d639613b8a7b612054506c88cdb719353f466ff") + version("3.1.0", sha256="4e7a7a36d07ed6f4f945afc4216db7f691d44a22b059c2404c917a160a687a6b") + + depends_on("python@3.7:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-numpy", type=("build", "run")) + depends_on("py-h5py", type=("build", "run")) + depends_on("py-biom-format", type=("build", "run")) + depends_on("py-biopython", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-hclust2", type=("build", "run"), when="@4.0.2:") + depends_on("py-requests", type=("build", "run")) + depends_on("py-dendropy", type=("build", "run")) + depends_on("py-pysam", type=("build", "run")) + depends_on("py-cmseq", type=("build", "run")) + depends_on("py-phylophlan", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("bowtie2@2.3:", type=("build", "run")) + depends_on("muscle@3.8.1551:", type=("build", "run")) + depends_on("blast-plus@2.6:", type=("build", "run")) + depends_on("raxml@8.2.10:", type=("build", "run")) + depends_on("samtools@1.9:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-phylophlan/package.py b/var/spack/repos/builtin/packages/py-phylophlan/package.py index 2baf08c8c2..26ea140813 100644 --- a/var/spack/repos/builtin/packages/py-phylophlan/package.py +++ b/var/spack/repos/builtin/packages/py-phylophlan/package.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack.package import * @@ -11,17 +12,25 @@ class PyPhylophlan(PythonPackage): phylogenetic profiling of genomes and metagenomes.""" homepage = "https://github.com/biobakery/phylophlan" - url = "https://github.com/biobakery/phylophlan/archive/refs/tags/3.0.2.tar.gz" + url = "https://github.com/biobakery/phylophlan/archive/refs/tags/3.0.3.tar.gz" + version("3.0.3", sha256="d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054") version("3.0.2", sha256="c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4") - depends_on("python@3:", type=("build", "run")) - depends_on("py-numpy@1.12.1:", type=("build", "run")) - depends_on("py-biopython@1.70:", type=("build", "run")) - depends_on("py-dendropy@4.2.0:", type=("build", "run")) - depends_on("muscle", type=("build", "run")) - depends_on("blast-plus", type=("build", "run")) - depends_on("diamond", type=("build", "run")) - depends_on("py-matplotlib", type=("build", "run")) - depends_on("py-pandas", type=("build", "run")) - depends_on("py-seaborn", type=("build", "run")) + depends_on("python@3.7:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-biopython@1.73:", type=("build", "run")) + depends_on("py-dendropy@4.4.0:", type=("build", "run")) + depends_on("py-matplotlib@3.1.0:", type=("build", "run")) + depends_on("py-numpy@1.15.4:", type=("build", "run")) + depends_on("py-pandas@0.24.2:", type=("build", "run")) + depends_on("py-seaborn@0.9.0:", type=("build", "run")) + depends_on("blast-plus@2.6.0:", type=("build", "run")) + depends_on("diamond@0.9:", type=("build", "run")) + depends_on("trimal@1.4.1:", type=("build", "run")) + depends_on("muscle@3.8.1551:", type=("build", "run")) + 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("mash", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py index ac1cec73f1..fb1bba14c5 100644 --- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py @@ -20,7 +20,7 @@ class PyPkgconfig(PythonPackage): depends_on("python@3.3:", when="@1.5.5:", type=("build", "run")) depends_on("python@2.7,3.3:", when="@1.5:", type=("build", "run")) depends_on("python@2.6:2.7,3.3:", when="@1.4:", type=("build", "run")) - depends_on("py-poetry-core@1:", when="@1.5.5:", type="build") - depends_on("py-poetry-core@0.12:", when="@1.5:", type="build") + depends_on("py-poetry-core@1:", when="@1.5.2:", type="build") + depends_on("py-poetry@0.12:", when="@1.5.0:1.5.1", type="build") depends_on("py-setuptools", when="@:1.4", type="build") depends_on("pkgconfig", type=("build", "run")) |