diff --git a/bio/vep/annotate/environment.yaml b/bio/vep/annotate/environment.yaml index 9a655b26ff..49b615ebb6 100644 --- a/bio/vep/annotate/environment.yaml +++ b/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 diff --git a/bio/vep/annotate/wrapper.py b/bio/vep/annotate/wrapper.py index d5e16df422..cced5dbf2a 100644 --- a/bio/vep/annotate/wrapper.py +++ b/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} " diff --git a/bio/vep/cache/environment.yaml b/bio/vep/cache/environment.yaml index 41325746dc..99ab298c53 100644 --- a/bio/vep/cache/environment.yaml +++ b/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 diff --git a/test.py b/test.py index 93bd0e9e79..f8446a606c 100644 --- a/test.py +++ b/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"], )