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packages: new versions (diamond, py-alive-progress, py-bakta, py-deepsig-biocomp), new packages (py-pyhmmer, py-pyrodigal) (#47277)

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* added updated versions
* added pyhmmer
* updated infernal
* fix blast-plus for apple-clang
* fix py-biopython build on apple-clang
* remove erroneous biopython dep: build issue is with python 3.8, not biopython
* deepsig python 3.9: expanding unnecessary python restrictions
* add pyrodigal
* fix unnecessarily strict diamond version
* builds and updates: blast-plus indexing broken, still need to test db download and bakta pipeline
* builds and runs
* revert blast-plus changes: remove my personal hacks to get blast-plus to build
This commit is contained in:
Luke Diorio-Toth 2024-11-11 20:13:46 -06:00 committed by GitHub
parent 37de92e7a2
commit 2987efa93c
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GPG Key ID: B5690EEEBB952194
6 changed files with 92 additions and 15 deletions
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1
var/spack/repos/builtin/packages/diamond/package.py
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@ -16,6 +16,7 @@ class Diamond(CMakePackage):
license("GPL-3.0-only")
version("2.1.10", sha256="c6ede5df30d9d496af314e740964c35a0e358458d9c8d9b8dd517d69828d9981")
version("2.1.9", sha256="4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88")
version("2.1.8", sha256="b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415")
version("2.1.7", sha256="2dcaba0e79ecb02c3d2a6816d317e714767118a9a056721643abff4c586ca95b")

5
var/spack/repos/builtin/packages/py-alive-progress/package.py
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@ -16,12 +16,15 @@ class PyAliveProgress(PythonPackage):
license("MIT")
version("3.2.0", sha256="ede29d046ff454fe56b941f686f89dd9389430c4a5b7658e445cb0b80e0e4deb")
version("2.4.1", sha256="089757c8197f27ad972ba27e1060f6db92368d83c736884e159034fd74865323")
version("1.6.2", sha256="642e1ce98becf226c8c36bf24e10221085998c5465a357a66fb83b7dc618b43e")
depends_on("python@2.7:3", type=("build", "run"))
depends_on("python@3.6:3", type=("build", "run"), when="@2:")
depends_on("python@3.7:3", type=("build", "run"), when="@2.2:")
depends_on("python@3.9:3", type=("build", "run"), when="@3.2:")
depends_on("py-setuptools", type="build")
depends_on("py-about-time@3.1.1", type=("build", "run"), when="@2.4.1:")
depends_on("py-about-time@3.1.1", type=("build", "run"), when="@2.4.1")
depends_on("py-about-time@4.2.1", type=("build", "run"), when="@3:")
depends_on("py-grapheme@0.6.0", type=("build", "run"), when="@2.4.1:")

43
var/spack/repos/builtin/packages/py-bakta/package.py
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@ -18,21 +18,42 @@ class PyBakta(PythonPackage):
license("GPL-3.0-only")
version("1.9.4", sha256="10330a10e459144dc78daa26f3a73674799706e2e1653e080366b1bbb9e5a5d9")
version("1.5.1", sha256="36781612c4eaa99e6e24a00e8ab5b27dadf21c98ae6d16432f3e78c96a4adb5d")
depends_on("python@3.8:", type=("build", "run"))
variant("deepsig", default=True, description="builds with deepsig to predict signal peptides")
depends_on("python@3.8:3.10", type=("build", "run"))
depends_on("py-setuptools", type=("build", "run"))
depends_on("py-biopython@1.78:", type=("build", "run"))
depends_on("py-xopen@1.1.0:", type=("build", "run"))
depends_on("py-xopen@1.5.0:", when="@1.8.2:", type=("build", "run"))
depends_on("py-xopen@1.1.0:", when="@:1.8.1", type=("build", "run"))
depends_on("py-requests@2.25.1:", type=("build", "run"))
depends_on("py-alive-progress@1.6.2", type=("build", "run"))
depends_on("trnascan-se@2.0.8:", type=("build", "run"))
depends_on("aragorn@1.2.38:", type=("build", "run"))
depends_on("py-alive-progress@3.0.1:", when="@1.7.0:", type=("build", "run"))
depends_on("py-alive-progress@1.6.2", when="@:1.6.1", type=("build", "run"))
depends_on("py-pyyaml@6.0:", when="@1.6.0:", type=("build", "run"))
depends_on("trnascan-se@2.0.11:", when="@1.6.0:", type=("build", "run"))
depends_on("trnascan-se@2.0.8:", when="@:1.5.1", type=("build", "run"))
depends_on("aragorn@1.2.41:", when="@1.7.0:", type=("build", "run"))
depends_on("aragorn@1.2.38:", when="@:1.6.1", type=("build", "run"))
depends_on("infernal@1.1.4:", type=("build", "run"))
depends_on("pilercr@1.06:", type=("build", "run"))
depends_on("prodigal@2.6.3:", type=("build", "run"))
depends_on("hmmer@3.3.2:", type=("build", "run"))
depends_on("diamond@2.0.14:", type=("build", "run"))
depends_on("blast-plus@2.12.0:", type=("build", "run"))
depends_on("amrfinder@3.10.23:", type=("build", "run"))
depends_on("py-deepsig-biocomp@1.2.5:", type=("build", "run"))
depends_on("py-pyrodigal@3.1.0:", when="@1.9.0:", type=("build", "run"))
depends_on("py-pyrodigal@2.1.0:", when="@1.7.0:1.8.2", type=("build", "run"))
depends_on("py-pyrodigal@2.0.2:", when="@1.6.0:1.6.1", type=("build", "run"))
depends_on("prodigal@2.6.3:", when="@:1.5.1", type=("build", "run"))
depends_on("hmmer@3.3.2:", when="@:1.8.1", type=("build", "run"))
depends_on("py-pyhmmer@0.10.4:", when="@1.9.4:", type=("build", "run"))
depends_on("py-pyhmmer@0.10.0:", when="@1.8.2:1.9.3", type=("build", "run"))
# known bug with diamond v2.1.9
# see https://github.com/oschwengers/bakta/issues/290
depends_on("diamond@2.1.8,2.1.10:", when="@1.9.0:", type=("build", "run"))
depends_on("diamond@2.0.14:", when="@:1.8.2", type=("build", "run"))
depends_on("blast-plus@2.14.0:", when="@1.9.0:", type=("build", "run"))
depends_on("blast-plus@2.12.0:", when="@:1.8.2", type=("build", "run"))
depends_on("amrfinder@3.11.26:", when="@1.9.0:", type=("build", "run"))
depends_on("amrfinder@3.10.23:", when="@1.5.1", type=("build", "run"))
depends_on("circos@0.69.8:", when="@1.6.0:", type=("build", "run"))
depends_on("py-deepsig-biocomp@1.2.5:", when="+deepsig", type=("build", "run"))
conflicts("platform=darwin", when="+deepsig")

6
var/spack/repos/builtin/packages/py-deepsig-biocomp/package.py
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@ -19,11 +19,11 @@ class PyDeepsigBiocomp(PythonPackage):
version("1.2.5", sha256="e954b815d63c221c564c7d3fe27123d7cd2c39b191d6107369ab095d506496e0")
depends_on("python@3.8", type=("build", "run"))
depends_on("python@3.8:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-biopython@1.78:", type=("build", "run"))
depends_on("py-keras@2.4.3", type=("build", "run"))
depends_on("py-tensorflow@2.2.0", type=("build", "run"))
depends_on("py-keras@2.4.3:", type=("build", "run"))
depends_on("py-tensorflow@2.2.0:", type=("build", "run"))
depends_on("py-tensorboard", type=("build", "run"))
@run_after("install")

27
var/spack/repos/builtin/packages/py-pyhmmer/package.py Normal file
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@ -0,0 +1,27 @@
# 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 PyPyhmmer(PythonPackage):
"""HMMER is a biological sequence analysis tool that uses profile hidden
Markov models to search for sequence homologs. HMMER3 is developed and
maintained by the Eddy/Rivas Laboratory at Harvard University. pyhmmer
is a Python package, implemented using the Cython language, that provides
bindings to HMMER3."""
homepage = "https://github.com/althonos/pyhmmer"
pypi = "pyhmmer/pyhmmer-0.10.14.tar.gz"
license("MIT", checked_by="luke-dt")
version("0.10.15", sha256="bf8e97ce8da6fb5850298f3074640f3e998d5a655877f865c1592eb057dc7921")
version("0.10.14", sha256="eb50bdfdf67a3b1fecfe877d7ca6d9bade9a9f3dea3ad60c959453bbb235573d")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools@46.4:", type="build")
depends_on("py-cython@3.0", type="build")
depends_on("py-psutil@5.8:", type=("build", "run"))

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var/spack/repos/builtin/packages/py-pyrodigal/package.py Normal file
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@ -0,0 +1,25 @@
# 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 PyPyrodigal(PythonPackage):
"""Cython bindings and Python interface to Prodigal, an ORF finder for
genomes and metagenomes"""
homepage = "https://github.com/althonos/pyrodigal"
pypi = "pyrodigal/pyrodigal-3.5.2.tar.gz"
license("GPL-3.0", checked_by="luke-dt")
version("3.5.2", sha256="2a40eb6113e720ada51c326958b295944cdc33ecee9f25d5bad4e9a8e6e6f7f5")
depends_on("c", type="build")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools@46.4:", type="build")
depends_on("py-archspec@0.2.0:", type="build")
depends_on("py-cython@3.0:", type=("build", "run"))