fix: upgrade vep wrappers to latest version, fixing issues with stric…

…t channel priorities. (#547)

* fix: upgrade vep wrappers to latest version, fixing issues with strict channel priorities.

* add encode package

* add encode-locale module

* dbg

* dbg

* add lwp-simple dep

* run verbose

* dbg

* dbg

* dbg

* dbg

* dbg

bio/vep/annotate/environment.yaml

@@ -3,5 +3,9 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - ensembl-vep =105
-  - bcftools =1.12
+  - ensembl-vep =107
+  - bcftools =1.15
+  # TODO remove once bioconda CDN has been updated to exclude
+  # broken unpinned perl-encode-locale packages
+  - perl-encode-locale=1.05=pl5321hdfd78af_7
+  - perl =5.32.1

bio/vep/annotate/wrapper.py

@@ -60,7 +60,7 @@ def get_only_child_dir(path):
     cache = (
         "--offline --cache --dir_cache {cache} --cache_version {release} --species {species} --assembly {build}"
     ).format(cache=cache, release=release, build=build, species=species)
-
+shell("conda list")
 shell(
     "(bcftools view '{snakemake.input.calls}' | "
     "vep {extra} {fork} "

bio/vep/cache/environment.yaml

@@ -3,6 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  # This version should not be changed unless the vep_install command needs an
-  # update or suddenly stops working.
-  - ensembl-vep =105
+  - ensembl-vep =107

test.py

@@ -4506,7 +4506,7 @@ def test_vep_plugins():
 def test_vep_annotate():
     run(
         "bio/vep/annotate",
-        ["snakemake", "--cores", "1", "variants.annotated.bcf", "--use-conda", "-F"],
+        ["snakemake", "--cores", "1", "variants.annotated.bcf", "--use-conda", "-F", "--verbose"],
     )