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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 * from spack.package import *
class Hybpiper(Package): class Hybpiper(PythonPackage, Package):
"""HybPiper was designed for targeted sequence capture, in which DNA """HybPiper was designed for targeted sequence capture, in which DNA
sequencing libraries are enriched for gene regions of interest, sequencing libraries are enriched for gene regions of interest,
especially for phylogenetics. HybPiper is a suite of Python scripts especially for phylogenetics. HybPiper is a suite of Python scripts
@ -17,24 +17,51 @@ class Hybpiper(Package):
homepage = "https://github.com/mossmatters/HybPiper" homepage = "https://github.com/mossmatters/HybPiper"
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz" url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
git = "https://github.com/mossmatters/HybPiper/HybPiper.git" git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
maintainers("snehring")
license("GPL-3.0-or-later") license("GPL-3.0-or-later")
version("2.1.8", sha256="ff358a560d6dbbec4fdac67457451cb4e6ca21b8661044c43902aa013d805e47")
version("1.3.1", sha256="7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf") version("1.3.1", sha256="7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf")
version("1.2.0", sha256="34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57") 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@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", 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")
depends_on("exonerate@2.4:", when="@2.1:")
depends_on("bbmap", when="@2.1:")
depends_on("blast-plus") depends_on("blast-plus")
depends_on("spades") depends_on("blast-plus@2.9.0:", when="@2.1:")
depends_on("parallel")
depends_on("bwa") depends_on("bwa")
depends_on("diamond", when="@2.1:")
depends_on("mafft", when="@2.1:")
depends_on("parallel")
depends_on("samtools") 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): def setup_run_environment(self, env):
env.set("HYBPIPER_HOME", self.prefix) env.set("HYBPIPER_HOME", self.prefix)
@when("@:1.3.1")
def install(self, spec, prefix): def install(self, spec, prefix):
mkdirp(prefix.bin) mkdirp(prefix.bin)
install("*.py", prefix.bin) install("*.py", prefix.bin)