fix: properly handle proxy setting in vep cache wrapper

bio/vep/cache/wrapper.py

@@ -1,21 +1,43 @@
 __author__ = "Johannes Köster"
-__copyright__ = "Copyright 2020, Johannes Köster"
+__copyright__ = "Copyright 2023, Johannes Köster"
 __email__ = "johannes.koester@uni-due.de"
 __license__ = "MIT"
 
+import tempfile
 from pathlib import Path
 from snakemake.shell import shell
 
+
 extra = snakemake.params.get("extra", "")
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
-shell(
-    "vep_install --AUTO cf "
-    "--SPECIES {snakemake.params.species} "
-    "--ASSEMBLY {snakemake.params.build} "
-    "--VERSION {snakemake.params.release} "
-    "--CACHEDIR {snakemake.output} "
-    "--CONVERT "
-    "--NO_UPDATE "
-    "{extra} {log}"
-)
+try:
+    release = int(snakemake.params.release)
+except ValueError:
+    raise ValueError("The parameter release is supposed to be an integer.")
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    # We download the cache tarball manually because vep_install does not consider proxy settings (in contrast to curl).
+    # See https://github.com/bcbio/bcbio-nextgen/issues/1080
+    vep_dir = "vep" if release >= 97 else "VEP"
+    cache_tarball = (
+        f"{snakemake.params.species}_vep_{release}_{snakemake.params.build}.tar.gz"
+    )
+    log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+    shell(
+        "curl -L ftp://ftp.ensembl.org/pub/release-{snakemake.params.release}/"
+        "variation/{vep_dir}/{cache_tarball} "
+        "-o {tmpdir}/{cache_tarball} {log}"
+    )
+
+    log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
+    shell(
+        "vep_install --AUTO cf "
+        "--SPECIES {snakemake.params.species} "
+        "--ASSEMBLY {snakemake.params.build} "
+        "--VERSION {release} "
+        "--CACHEURL {tmpdir} "
+        "--CACHEDIR {snakemake.output} "
+        "--CONVERT "
+        "--NO_UPDATE "
+        "{extra} {log}"
+    )