vep-cache: new package (#44523)
* py-uvloop: add v3.8.14, v3.9.15, v3.10.3 and dependencies * rollback * vep: add v110,v111,v112 * vep-cache: add v110,v111,v112 * Cleanup * Reorganizigng Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Update package.py * Update package.py * [@spackbot] updating style on behalf of teaguesterling * Update package.py * Update package.py * Update package.py * [@spackbot] updating style on behalf of teaguesterling * Update package.py * [@spackbot] updating style on behalf of teaguesterling * Fix scoping and syntax issues Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * fix styles Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * fix variants * fixing up variant issues and cleaning up resource code Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * fixing unused imports Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Apply suggestions from code review Co-authored-by: Arne Becker <101113822+EbiArnie@users.noreply.github.com> * fixing vep dependencies Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Fixing resources Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Fixing issue where resources are not downloaded Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * vep-cache fixing downloads Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * defaulting to using VEP installer Signed-off-by: Teague Sterling <teaguesterling@gmail.com> * Removing resource-based cache installation and simplifying package. Resources without checksums doesn't work (anymore?) and calculating them with be difficult Signed-off-by: Teague Sterling <teaguesterling@gmail.com> --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com> Co-authored-by: Arne Becker <101113822+EbiArnie@users.noreply.github.com>
This commit is contained in:
Teague Sterling
GitHub
parent
c9ed91758d
commit
10f7014add
151
var/spack/repos/builtin/packages/vep-cache/package.py
Normal file
151
var/spack/repos/builtin/packages/vep-cache/package.py
Normal file
@ -0,0 +1,151 @@
|
||||
# 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 VepCache(Package):
|
||||
"""Separate installation and management for the Ensembl Variant Effect Predictor (vep)"""
|
||||
|
||||
homepage = "https://useast.ensembl.org/info/docs/tools/vep/index.html"
|
||||
maintainers("teaguesterling")
|
||||
# This is a dummy value to get spack to resolve resources, which are not downloaded
|
||||
# when has_code = False
|
||||
has_code = False
|
||||
|
||||
license("Apache-2.0", checked_by="teaguesterling")
|
||||
|
||||
vep_versions = ["112", "111", "110"]
|
||||
depends_on("vep", type="build")
|
||||
for major in vep_versions:
|
||||
version(major)
|
||||
depends_on(f"vep@{major}", type="build", when=f"@{major}+match_vep_version")
|
||||
|
||||
vep_assembly_sources = ["ensembl", "refseq", "merged"]
|
||||
|
||||
# This is an incomplete list
|
||||
vep_species = {
|
||||
"bos_taurus": ["UMD3.1"],
|
||||
"danio_rerio": ["GRCz11"],
|
||||
"homo_sapiens": ["GRCh38", "GRCh37"],
|
||||
"mus_musculus": ["GRCm38"],
|
||||
"rattus_norvegicus": ["Rnor_6.0"],
|
||||
}
|
||||
|
||||
variant("match_vep_version", default=True, description="Match cache and software version")
|
||||
variant("env", default=True, description="Setup VEP environment variables for this cache")
|
||||
|
||||
# Cache configuration options
|
||||
variant("fasta", default=True, description="Add FASTA files to the cache")
|
||||
variant("indexed", default=True, description="Use indexed cache")
|
||||
|
||||
variant(
|
||||
"assembly_source",
|
||||
values=vep_assembly_sources,
|
||||
default="ensembl",
|
||||
description="What reference genome source",
|
||||
)
|
||||
variant(
|
||||
"species",
|
||||
values=vep_species.keys(),
|
||||
default="homo_sapiens",
|
||||
description="Which species to download the cache for (only one at a time)",
|
||||
)
|
||||
variant(
|
||||
"assembly",
|
||||
values=["latest"]
|
||||
+ [
|
||||
conditional(*assemblies, when=f"species={species}")
|
||||
for species, assemblies in vep_species.items()
|
||||
],
|
||||
default="latest",
|
||||
multi=False,
|
||||
description="Which assembly of genome to use (only needed for homo sapiens)",
|
||||
)
|
||||
|
||||
def cache_from_spec(self, spec):
|
||||
variants = spec.variants
|
||||
indexed = spec.satisfies("+indexed")
|
||||
cache_type = variants["assembly_source"].value
|
||||
species = variants["species"].value
|
||||
assembly = variants["assembly"].value
|
||||
assembly = self.vep_species[species][0] if assembly == "latest" else assembly
|
||||
return indexed, cache_type, species, assembly
|
||||
|
||||
def vep_cache_config(self, base):
|
||||
spec = self.spec
|
||||
cache_version = spec.version.up_to(1)
|
||||
indexed, cache_type, species, assembly = self.cache_from_spec(spec)
|
||||
user_root = join_path(base, "share", "vep")
|
||||
root = user_root # Should this be VEP install dir?
|
||||
|
||||
suffix = "" if cache_type == "ensembl" else f"_{cache_type}"
|
||||
species_cache = f"{species}{suffix}"
|
||||
|
||||
if species == "homo_sapiens":
|
||||
cache_dir = join_path(species, f"{cache_version}_{assembly}")
|
||||
else:
|
||||
cache_dir = join_path(species, f"{cache_version}")
|
||||
|
||||
return {
|
||||
"root": root,
|
||||
"user_root": user_root,
|
||||
"version": f"{cache_version}",
|
||||
"type": f"{cache_type}",
|
||||
"species": species,
|
||||
"cache_species": species_cache,
|
||||
"assembly": f"{assembly}",
|
||||
"indexed": indexed,
|
||||
"dir": cache_dir,
|
||||
"full_path": join_path(root, cache_dir),
|
||||
}
|
||||
|
||||
def setup_run_environment(self, env):
|
||||
if self.spec.satisfies("+env"):
|
||||
cache = self.vep_cache_config(self.home)
|
||||
env.set("VEP_OFFLINE", "1")
|
||||
env.set("VEP_CACHE", "1")
|
||||
env.set("VEP_DIR", cache["user_root"])
|
||||
env.set("VEP_SPECIES", cache["species"])
|
||||
env.set("VEP_CACHE_VERSION", cache["version"])
|
||||
if cache["assembly"] is not None:
|
||||
env.set("VEP_ASSEMBLY", cache["assembly"])
|
||||
if cache["type"] == "refseq":
|
||||
env.set("VEP_REFSEQ", "1")
|
||||
if cache["type"] == "merged":
|
||||
env.set("VEP_MERGED", "1")
|
||||
if self.spec.satisfies("+fasta"):
|
||||
pass
|
||||
|
||||
def cache_installer_args(self):
|
||||
cache = self.vep_cache_config(self.prefix)
|
||||
args = [
|
||||
"--CACHEDIR",
|
||||
cache["full_path"],
|
||||
"--CACHE_VERSION",
|
||||
cache["version"],
|
||||
"--SPECIES",
|
||||
cache["cache_species"],
|
||||
]
|
||||
if cache["species"] == "homo_sapiens":
|
||||
args += ["--ASSEMBLY", cache["assembly"]]
|
||||
|
||||
return args
|
||||
|
||||
def installer_args(self):
|
||||
auto = "cf" if self.spec.satisfies("+fasta") else "c"
|
||||
args = ["--AUTO", auto, "--NO_UPDATE", "--NO_TEST"]
|
||||
args += self.cache_installer_args()
|
||||
return args
|
||||
|
||||
def install_with_installer(self):
|
||||
vep = self.spec["vep"].package
|
||||
installer = which(vep.vep_installer_path)
|
||||
installer(*self.installer_args())
|
||||
|
||||
def install(self, spec, prefix):
|
||||
cache = self.vep_cache_config(self.prefix)
|
||||
mkdirp(cache["full_path"])
|
||||
self.install_with_installer()
|
||||
Loading…
Reference in New Issue
Block a user