From 046fa3958223ce4542578ef26502d39f4c5d71ef Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 2 Jun 2022 16:09:09 +0200 Subject: [PATCH 1/3] update VEP version + cache --- modules/ensemblvep/Dockerfile | 4 ++-- modules/ensemblvep/build.sh | 12 ++++++------ modules/ensemblvep/environment.yml | 4 ++-- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/ensemblvep/Dockerfile b/modules/ensemblvep/Dockerfile index b4a1c664..4ada7c6b 100644 --- a/modules/ensemblvep/Dockerfile +++ b/modules/ensemblvep/Dockerfile @@ -11,8 +11,8 @@ RUN conda env create -f /environment.yml && conda clean -a # Setup default ARG variables ARG GENOME=GRCh38 ARG SPECIES=homo_sapiens -ARG VEP_VERSION=104 -ARG VEP_TAG=104.3 +ARG VEP_VERSION=105 +ARG VEP_TAG=105.0 # Add conda installation dir to PATH (instead of doing 'conda activate') ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh index 650c8704..402f2434 100755 --- a/modules/ensemblvep/build.sh +++ b/modules/ensemblvep/build.sh @@ -20,9 +20,9 @@ build_push() { docker push nfcore/vep:${VEP_TAG}.${GENOME} } -build_push "GRCh37" "homo_sapiens" "104" "104.3" -build_push "GRCh38" "homo_sapiens" "104" "104.3" -build_push "GRCm38" "mus_musculus" "102" "104.3" -build_push "GRCm39" "mus_musculus" "104" "104.3" -build_push "CanFam3.1" "canis_lupus_familiaris" "104" "104.3" -build_push "WBcel235" "caenorhabditis_elegans" "104" "104.3" +build_push "GRCh37" "homo_sapiens" "105" "105.0" +build_push "GRCh38" "homo_sapiens" "105" "105.0" +build_push "GRCm38" "mus_musculus" "102" "105.0" +build_push "GRCm39" "mus_musculus" "105" "105.0" +build_push "CanFam3.1" "canis_lupus_familiaris" "105" "105.0" +build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" diff --git a/modules/ensemblvep/environment.yml b/modules/ensemblvep/environment.yml index c0731c26..5df85b80 100644 --- a/modules/ensemblvep/environment.yml +++ b/modules/ensemblvep/environment.yml @@ -1,10 +1,10 @@ # You can use this file to create a conda environment for this module: # conda env create -f environment.yml -name: nf-core-vep-104.3 +name: nf-core-vep-105.0 channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::ensembl-vep=104.3 + - bioconda::ensembl-vep=105.0 From bc0f52bcd3a64f27d8fb2da3a6424b427e15e53c Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 2 Jun 2022 16:11:11 +0200 Subject: [PATCH 2/3] fix cache version --- modules/ensemblvep/build.sh | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh index 402f2434..e21a7c0d 100755 --- a/modules/ensemblvep/build.sh +++ b/modules/ensemblvep/build.sh @@ -20,9 +20,9 @@ build_push() { docker push nfcore/vep:${VEP_TAG}.${GENOME} } -build_push "GRCh37" "homo_sapiens" "105" "105.0" -build_push "GRCh38" "homo_sapiens" "105" "105.0" -build_push "GRCm38" "mus_musculus" "102" "105.0" -build_push "GRCm39" "mus_musculus" "105" "105.0" -build_push "CanFam3.1" "canis_lupus_familiaris" "105" "105.0" -build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" +# build_push "GRCh37" "homo_sapiens" "105" "105.0" +# build_push "GRCh38" "homo_sapiens" "105" "105.0" +# build_push "GRCm38" "mus_musculus" "102" "105.0" +# build_push "GRCm39" "mus_musculus" "105" "105.0" +build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0" +# build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" From b623ff5d2798b8c955baeb3890f0baee6077db66 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 2 Jun 2022 16:11:45 +0200 Subject: [PATCH 3/3] fix comments --- modules/ensemblvep/build.sh | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh index e21a7c0d..6f340c0f 100755 --- a/modules/ensemblvep/build.sh +++ b/modules/ensemblvep/build.sh @@ -20,9 +20,9 @@ build_push() { docker push nfcore/vep:${VEP_TAG}.${GENOME} } -# build_push "GRCh37" "homo_sapiens" "105" "105.0" -# build_push "GRCh38" "homo_sapiens" "105" "105.0" -# build_push "GRCm38" "mus_musculus" "102" "105.0" -# build_push "GRCm39" "mus_musculus" "105" "105.0" +build_push "GRCh37" "homo_sapiens" "105" "105.0" +build_push "GRCh38" "homo_sapiens" "105" "105.0" +build_push "GRCm38" "mus_musculus" "102" "105.0" +build_push "GRCm39" "mus_musculus" "105" "105.0" build_push "CanFam3.1" "canis_lupus_familiaris" "104" "105.0" -# build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0" +build_push "WBcel235" "caenorhabditis_elegans" "105" "105.0"