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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/vep/package.py | 131 |
1 files changed, 131 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/vep/package.py b/var/spack/repos/builtin/packages/vep/package.py new file mode 100644 index 0000000000..5f60345277 --- /dev/null +++ b/var/spack/repos/builtin/packages/vep/package.py @@ -0,0 +1,131 @@ +# 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 Vep(Package): + """ + Ensembl Variant Effect Predictor (VEP) determines the effect of your variants + (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, + and protein sequence, as well as regulatory regions. + (Requires addtional data available via the `vep-cache` package) + """ + + homepage = "https://useast.ensembl.org/info/docs/tools/vep/index.html" + url = "https://github.com/Ensembl/ensembl-vep/archive/release/111.zip" + + maintainers("teaguesterling") + + license("APACHE-2.0", checked_by="teaguesterling") + + version("112.0", sha256="46dd08838fd94ecbfaa931266c78570748a3cb39668b6e43c3608e6cd0aff93f") + version("111.0", sha256="9cb326a1fa0054ce1a417f8fd4f2325ba605c40ec10eefbf87f461c264a89407") + version("110.0", sha256="391a1fe50139064c1044c09e013bb21437933d677537b5d3336807f3b131fb51") + + variant("vep_installer", default=False, description="Install dependencies with VEP installer") + variant("utility_scripts", default=True, description="Install utility scripts") + + # Optional dependencies + variant("json", default=True, description="Include requirements for JSON support") + variant("nearest", default=True, description="Include requirements for 'nearest'") + variant("gzip", default=True, description="Include requirements for gzip support") + + # Bundled versions + variant("bundled_bioperl", default=False, description="Build with bundled BioPerl") + variant("bundled_htslib", default=False, description="Build with bundled HTSLib") + + extends("perl") + + with default_args(type="build"): + depends_on("gcc", when="+vep_installer") + depends_on("gmake") + + with default_args(type=("build", "run")): + depends_on("perl@5.10:") + depends_on("perl-archive-zip") + depends_on("perl-dbd-mysql") + depends_on("perl-dbi") + depends_on("perl-bio-db-hts") + depends_on("perl-json", when="+json") + depends_on("perl-set-intervaltree", when="+nearest") + depends_on("perl-perlio-gzip", when="+gzip") + depends_on("perl-bioperl@1.6:", when="~bundled_bioperl") + depends_on("htslib@1.9:", when="~bundled_htslib") + + # This is a workaround for the VEP installer which downloads + # and manually installs dependent packages + with default_args(type=("build", "run"), when="~vep_installer"): + for ver in ["110", "111", "112"]: + depends_on(f"perl-bio-ensembl@{ver}", when=f"@{ver}") + depends_on(f"perl-bio-ensembl-variation@{ver}", when=f"@{ver}") + depends_on(f"perl-bio-ensembl-funcgen@{ver}", when=f"@{ver}") + depends_on(f"perl-bio-ensembl-io@{ver}", when=f"@{ver}") + + # These should probably move futher up the dependency stack + conflicts("zlib-ng", when="+gzip") + conflicts("zlib-ng", when="+bundled_htslib") + + @property + def vep_lib_path(self): + return self.prefix.lib.perl5 + + @property + def vep_share_path(self): + return self.prefix.share.vep + + @property + def vep_scripts_path(self): + return self.vep_share_path.scripts + + @property + def vep_installer_path(self): + return f"{self.vep_scripts_path.INSTALL}.pl" + + def setup_run_environment(self, env): + env.set("VEP_HOME", self.home) + if self.spec.satisfies("+bundled_htslib"): + env.prepend_path("PATH", self.vep_lib_path.htslib) + + def installer_args(self): + auto = "a" + args = ["--DESTDIR", f"{self.vep_lib_path}", "--NO_UPDATE", "--NO_TEST"] + if self.spec.satisfies("~bundled_htslib"): + args += ["--NO_HTSLIB"] + if self.spec.satisfies("~bundled_bioperl"): + args += ["--NO_BIOPERL"] + args += ["--AUTO", auto] + return args + + def install(self, spec, prefix): + mkdirp(self.prefix.bin) + mkdirp(self.vep_lib_path) + mkdirp(self.vep_share_path) + mkdirp(self.vep_scripts_path) + + # Add the VEP perl modules and executable + install_tree("modules", self.vep_lib_path) + install("vep", prefix.bin.vep) + + # We save this so it can be used later to update caches + # and use to do the rest of the install, if requested + install("INSTALL.pl", self.vep_installer_path) + + # This is required for any cache updating via the installer + install("convert_cache.pl", self.vep_scripts_path) + + # Resolve dependencies via VEP installer if desired + if spec.satisfies("+vep_installer"): + # If we don't do this a bunch of perl libs will be missing + # Run the customer VEP installer/downloader, which downloads + # copies a bunch of additional perl modules + installer = which(self.vep_installer_path) + installer(*self.installer_args()) + + # Manually install auxilary scripts if requested + if self.spec.satisfies("+utility_scripts"): + install("filter_vep", prefix.bin.filter_vep) + install("haplo", prefix.bin.haplo) + install("variant_recoder", prefix.bin.variant_recoder) |