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hybpiper: change package type, add version 2.1.8 (#45262)

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Signed-off-by: Shane Nehring <snehring@iastate.edu>
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snehring 2024-07-24 09:16:54 -05:00 committed by GitHub
parent e529a454eb
commit 39455768b2
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1 changed files with 30 additions and 3 deletions
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33
var/spack/repos/builtin/packages/hybpiper/package.py
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@ -7,7 +7,7 @@
from spack.package import *
class Hybpiper(Package):
class Hybpiper(PythonPackage, Package):
"""HybPiper was designed for targeted sequence capture, in which DNA
sequencing libraries are enriched for gene regions of interest,
especially for phylogenetics. HybPiper is a suite of Python scripts
@ -17,24 +17,51 @@ class Hybpiper(Package):
homepage = "https://github.com/mossmatters/HybPiper"
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
maintainers("snehring")
license("GPL-3.0-or-later")
version("2.1.8", sha256="ff358a560d6dbbec4fdac67457451cb4e6ca21b8661044c43902aa013d805e47")
version("1.3.1", sha256="7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf")
version("1.2.0", sha256="34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57")
build_system(
conditional("python_pip", when="@2.1:"),
conditional("generic", when="@:1.3.1"),
default="python_pip",
)
depends_on("python@2.7:", type=("build", "run"))
depends_on("python@3.9:", type=("build", "run"), when="@2.1:")
depends_on("py-biopython", type=("build", "run"))
depends_on("py-biopython@1.80:", type=("build", "run"), when="@2.1:")
depends_on("py-matplotlib", type=("build", "run"), when="@2.1:")
depends_on("py-pandas", type=("build", "run"), when="@2.1:")
depends_on("py-pebble", type=("build", "run"), when="@2.1:")
depends_on("py-progressbar2", type=("build", "run"), when="@2.1:")
depends_on("py-psutil", type=("build", "run"), when="@2.1:")
depends_on("py-scipy", type=("build", "run"), when="@2.1:")
depends_on("py-seaborn", type=("build", "run"), when="@2.1:")
depends_on("exonerate")
depends_on("exonerate@2.4:", when="@2.1:")
depends_on("bbmap", when="@2.1:")
depends_on("blast-plus")
depends_on("spades")
depends_on("parallel")
depends_on("blast-plus@2.9.0:", when="@2.1:")
depends_on("bwa")
depends_on("diamond", when="@2.1:")
depends_on("mafft", when="@2.1:")
depends_on("parallel")
depends_on("samtools")
depends_on("samtools@1.14", when="@2.1:")
depends_on("spades")
depends_on("spades@3.15.4:", when="@2.1:")
def setup_run_environment(self, env):
env.set("HYBPIPER_HOME", self.prefix)
@when("@:1.3.1")
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("*.py", prefix.bin)