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>

1 files changed, 151 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/vep-cache/package.py b/var/spack/repos/builtin/packages/vep-cache/package.py
new file mode 100644
index 0000000000..6e84426a52
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vep-cache/package.py
@@ -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()