1e1cb68b84
* Add audit check to spot when= arguments using named specs * Fix package issues caught by the new audit
130 lines
5.5 KiB
Python
130 lines
5.5 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Interproscan(Package):
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"""InterProScan is the software package that allows sequences
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(protein and nucleic) to be scanned against InterPro's signatures.
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Signatures are predictive models, provided by several different
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databases, that make up the InterPro consortium. By default this
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does not download all the databases you likely want, you'll either
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want to build with +databases or download the data archive for the
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version you installed to a separate location and modify interproscan.properties"""
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homepage = "https://www.ebi.ac.uk/interpro/interproscan.html"
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url = "https://github.com/ebi-pf-team/interproscan/archive/5.36-75.0.tar.gz"
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maintainers("snehring")
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version("5.63-95.0", sha256="3d7babd09e64da3d7104c58f1e5104a298d69425e3210952331bc3f1ddf89ca6")
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version("5.61-93.0", sha256="70aca3b14983733fe5119b6978cb707156d006d7f737aa60ce6c9addd6c288e4")
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version("5.56-89.0", sha256="75e6a8f86ca17356a2f77f75b07d6d8fb7b397c9575f6e9716b64983e490b230")
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version("5.38-76.0", sha256="cb191ff8eee275689b789167a57b368ea5c06bbcd36b4de23e8bbbbdc0fc7434")
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version("5.36-75.0", sha256="383d7431e47c985056c856ceb6d4dcf7ed2559a4a3d5c210c01ce3975875addb")
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version(
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"4.8",
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sha256="f1cb0ae1218eb05ed59ad7f94883f474eb9a6185a56ad3a93a364acb73506a3f",
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url="ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/4/RELEASE/4.8/iprscan_v4.8.tar.gz",
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)
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resource(
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when="@5.63-95.0 +databases",
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name="databases",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/5.63-95.0/alt/interproscan-data-5.63-95.0.tar.gz",
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sha256="6048eabe2eeaa4630b7a6a0b34d8c5a1724b0d22bba318c04c43777368e16cc4",
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)
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resource(
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when="@5.61-93.0 +databases",
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name="databases",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/5.61-93.0/alt/interproscan-data-5.61-93.0.tar.gz",
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sha256="064aa4b4c3b2e27b457298359087878e48fc785bff801c95691f090d1b83867d",
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)
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resource(
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when="@5.56-89.0 +databases",
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name="databases",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/5.56-89.0/alt/interproscan-data-5.56-89.0.tar.gz",
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sha256="49cd0c69711f9469f3b68857f4581b23ff12765ca2b12893d18e5a9a5cd8032d",
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)
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resource(
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when="@5.38-76.0 +databases",
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name="databases",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/5.38-76.0/alt/interproscan-data-5.38-76.0.tar.gz",
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sha256="e05e15d701037504f92ecf849c20317e70df28e78ff1945826b3c1e16d9b9cce",
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)
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resource(
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when="@5.36-75.0 +databases",
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name="databases",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/5/5.36-75.0/alt/interproscan-data-5.36-75.0.tar.gz",
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sha256="e9b1e6f2d1c20d06661a31a08c973bc8ddf039a4cf1e45ec4443200375e5d6a4",
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)
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resource(
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when="@:4.8",
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name="binaries",
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url="https://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/iprscan_bin4.x_Linux64.tar.gz",
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sha256="551610a4682b112522f3ded5268f76ba9a47399a72e726fafb17cc938a50e7ee",
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)
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variant(
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"databases",
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default=False,
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description="Fetch and include databases in the install. Greatly increases install size.",
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)
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depends_on("java@8.0:8.9", type=("build", "run"), when="@5:5.36-99.0")
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depends_on("java@11", type=("build", "run"), when="@5.37-76.0:")
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depends_on("maven", type="build", when="@5:")
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depends_on("perl@5:", type=("build", "run"))
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depends_on("python@3:", when="@5:", type=("build", "run"))
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depends_on("perl-cgi", when="@:4.8", type=("build", "run"))
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depends_on("perl-mailtools", when="@:4.8", type=("build", "run"))
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depends_on("perl-xml-quote", when="@:4.8", type=("build", "run"))
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depends_on("perl-xml-parser", when="@:4.8", type=("build", "run"))
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depends_on("perl-io-string", when="@:4.8", type=("build", "run"))
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depends_on("perl-io-stringy", when="@:4.8", type=("build", "run"))
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depends_on("perl-db-file", when="@:4.8", type=("build", "run"))
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patch("large-gid.patch", when="@5:")
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patch("non-interactive.patch", when="@:4.8")
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patch("ps_scan.patch", when="@:4.8")
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patch("web-pom.patch", when="@5:")
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def install(self, spec, prefix):
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with working_dir("core"):
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if self.run_tests:
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which("mvn")("verify")
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else:
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which("mvn")("clean", "install", "-DskipTests")
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with working_dir("jms-implementation"):
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which("mvn")("clean", "package", "-DskipTests")
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target = join_path("core", "jms-implementation", "target", "interproscan-5-dist")
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install_tree(target, prefix)
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if spec.satisfies("+databases"):
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remove_directory_contents(prefix.data)
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install_tree(f"interproscan-{self.spec.version}/data", prefix.data)
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# link the main shell script into the PATH
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symlink(join_path(prefix, "interproscan.sh"), join_path(prefix.bin, "interproscan.sh"))
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@when("@:4.8")
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def install(self, spec, prefix):
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perl = which("perl")
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src = join_path(self.stage.source_path, "iprscan", "bin", "Linux")
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dst = join_path(self.stage.source_path, "bin", "binaries")
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force_symlink(src, dst)
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install_tree(".", prefix)
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with working_dir(prefix):
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perl("Config.pl")
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