vep: new package (#44522)
* Adding the perl-bio-db-bigfile package * Adding perl-bio-ensembl package * Adding perl-bio-ensembl-variation package * Adding the perl-bio-ensembl-funcgen package * Adding perl-bio-ensembl-io package * Fixing checksums * py-uvloop: add v3.8.14, v3.9.15, v3.10.3 and dependencies * rollback * Update package.py * Update package.py * vep: add v110,v111,v112 * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Updating dependent package handling Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update package.py * Update package.py * Reverting variants Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update package.py * Update package.py * Rename package.py to package.py * Update package.py * Update package.py * Update package.py * Fix variant installation and dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Styles Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Removing unneeded dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com> Co-authored-by: Bernhard Kaindl <contact@bernhard.kaindl.dev>
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Teague Sterling
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var/spack/repos/builtin/packages/vep/package.py
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var/spack/repos/builtin/packages/vep/package.py
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# Copyright 2013-2024 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 Vep(Package):
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"""
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Ensembl Variant Effect Predictor (VEP) determines the effect of your variants
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(SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts,
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and protein sequence, as well as regulatory regions.
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(Requires addtional data available via the `vep-cache` package)
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"""
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homepage = "https://useast.ensembl.org/info/docs/tools/vep/index.html"
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url = "https://github.com/Ensembl/ensembl-vep/archive/release/111.zip"
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maintainers("teaguesterling")
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license("APACHE-2.0", checked_by="teaguesterling")
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version("112.0", sha256="46dd08838fd94ecbfaa931266c78570748a3cb39668b6e43c3608e6cd0aff93f")
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version("111.0", sha256="9cb326a1fa0054ce1a417f8fd4f2325ba605c40ec10eefbf87f461c264a89407")
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version("110.0", sha256="391a1fe50139064c1044c09e013bb21437933d677537b5d3336807f3b131fb51")
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variant("vep_installer", default=False, description="Install dependencies with VEP installer")
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variant("utility_scripts", default=True, description="Install utility scripts")
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# Optional dependencies
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variant("json", default=True, description="Include requirements for JSON support")
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variant("nearest", default=True, description="Include requirements for 'nearest'")
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variant("gzip", default=True, description="Include requirements for gzip support")
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# Bundled versions
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variant("bundled_bioperl", default=False, description="Build with bundled BioPerl")
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variant("bundled_htslib", default=False, description="Build with bundled HTSLib")
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extends("perl")
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with default_args(type="build"):
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depends_on("gcc", when="+vep_installer")
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depends_on("gmake")
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with default_args(type=("build", "run")):
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depends_on("perl@5.10:")
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depends_on("perl-archive-zip")
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depends_on("perl-dbd-mysql")
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depends_on("perl-dbi")
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depends_on("perl-bio-db-hts")
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depends_on("perl-json", when="+json")
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depends_on("perl-set-intervaltree", when="+nearest")
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depends_on("perl-perlio-gzip", when="+gzip")
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depends_on("perl-bioperl@1.6:", when="~bundled_bioperl")
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depends_on("htslib@1.9:", when="~bundled_htslib")
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# This is a workaround for the VEP installer which downloads
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# and manually installs dependent packages
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with default_args(type=("build", "run"), when="~vep_installer"):
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for ver in ["110", "111", "112"]:
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depends_on(f"perl-bio-ensembl@{ver}", when=f"@{ver}")
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depends_on(f"perl-bio-ensembl-variation@{ver}", when=f"@{ver}")
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depends_on(f"perl-bio-ensembl-funcgen@{ver}", when=f"@{ver}")
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depends_on(f"perl-bio-ensembl-io@{ver}", when=f"@{ver}")
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# These should probably move futher up the dependency stack
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conflicts("zlib-ng", when="+gzip")
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conflicts("zlib-ng", when="+bundled_htslib")
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@property
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def vep_lib_path(self):
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return self.prefix.lib.perl5
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@property
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def vep_share_path(self):
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return self.prefix.share.vep
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@property
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def vep_scripts_path(self):
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return self.vep_share_path.scripts
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@property
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def vep_installer_path(self):
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return f"{self.vep_scripts_path.INSTALL}.pl"
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def setup_run_environment(self, env):
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env.set("VEP_HOME", self.home)
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if self.spec.satisfies("+bundled_htslib"):
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env.prepend_path("PATH", self.vep_lib_path.htslib)
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def installer_args(self):
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auto = "a"
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args = ["--DESTDIR", f"{self.vep_lib_path}", "--NO_UPDATE", "--NO_TEST"]
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if self.spec.satisfies("~bundled_htslib"):
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args += ["--NO_HTSLIB"]
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if self.spec.satisfies("~bundled_bioperl"):
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args += ["--NO_BIOPERL"]
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args += ["--AUTO", auto]
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return args
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def install(self, spec, prefix):
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mkdirp(self.prefix.bin)
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mkdirp(self.vep_lib_path)
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mkdirp(self.vep_share_path)
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mkdirp(self.vep_scripts_path)
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# Add the VEP perl modules and executable
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install_tree("modules", self.vep_lib_path)
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install("vep", prefix.bin.vep)
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# We save this so it can be used later to update caches
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# and use to do the rest of the install, if requested
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install("INSTALL.pl", self.vep_installer_path)
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# This is required for any cache updating via the installer
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install("convert_cache.pl", self.vep_scripts_path)
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# Resolve dependencies via VEP installer if desired
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if spec.satisfies("+vep_installer"):
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# If we don't do this a bunch of perl libs will be missing
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# Run the customer VEP installer/downloader, which downloads
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# copies a bunch of additional perl modules
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installer = which(self.vep_installer_path)
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installer(*self.installer_args())
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# Manually install auxilary scripts if requested
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if self.spec.satisfies("+utility_scripts"):
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install("filter_vep", prefix.bin.filter_vep)
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install("haplo", prefix.bin.haplo)
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install("variant_recoder", prefix.bin.variant_recoder)
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