diff --git a/.bumpversion.cfg b/.bumpversion.cfg index e11909d..6b53ecc 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -4,3 +4,5 @@ commit = True tag = False [bumpversion:file:setup.py] + +[bumpversion:file:Dockerfile] diff --git a/Dockerfile b/Dockerfile index fb08987..00afd29 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,4 +15,4 @@ RUN apt update && apt install -y \ rm -r /var/lib/apt/lists/* && \ rm -r /var/cache/apt/* -RUN pip install --no-cache-dir git+https://github.com/populationgenomics/automated-interpretation-pipeline.git@${RELEASE} +RUN pip install --no-cache-dir git+https://github.com/populationgenomics/ClinvArbitration.git@${RELEASE} diff --git a/data/pathogenic_annotated.vcf.bgz b/data/pathogenic_annotated.vcf.bgz new file mode 100644 index 0000000..20030d8 Binary files /dev/null and b/data/pathogenic_annotated.vcf.bgz differ diff --git a/data/pathogenic_annotated.vcf.bgz.tbi b/data/pathogenic_annotated.vcf.bgz.tbi new file mode 100644 index 0000000..98eb0f7 Binary files /dev/null and b/data/pathogenic_annotated.vcf.bgz.tbi differ diff --git a/example_script.sh b/example_script.sh index 73bfe94..b6575f7 100644 --- a/example_script.sh +++ b/example_script.sh @@ -3,7 +3,7 @@ set -ex # create a docker image from this repository -docker build --platform linux/arm64/v8 -t hail_clinvar:example --platform linux/amd64 . +docker build --platform linux/arm64/v8 -t clinvarbitration:example --platform linux/amd64 . # make local copies of the NCBI data files required as input using wget # create a directory called data, if one doesn't already exist @@ -14,7 +14,7 @@ fi #wget -O data/submission_summary.txt.gz https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/submission_summary.txt.gz # run the docker image to generate the summarised output -docker run -v "$(pwd)/data":/data hail_clinvar:example \ +docker run -v "$(pwd)/data":/data clinvarbitration:example \ resummary -v "/data/variant_summary.txt.gz" -s "/data/submission_summary.txt.gz" -o "/data/clinvar_summary" --minimal # upon completion, this will have generated files in the data directory: @@ -26,8 +26,8 @@ docker run -v "$(pwd)/data":/data hail_clinvar:example \ ## This is where you should run VEP on data/clinvar_summary.vcf.bgz, with protein consequence annotation per transcript ## Let's imagine you did that, and the result is in data/pathogenic_annotated.vcf.bgz ## I've enclosed a 10-variant example of this, as annotated by https://www.ensembl.org/Homo_sapiens/Tools/VEP -#docker run --platform linux/amd64 -v "$(pwd)/data":/data hail_clinvar:example \ -# /bin/bash -c "python3 /clinvarbitration/clinvar_by_codon_from_vcf.py -i /data/pathogenic_annotated.vcf.bgz -o /data/pm5" +#docker run --platform linux/amd64 -v "$(pwd)/data":/data clinvarbitration:example \ +# /bin/bash -c "python3 /clinvarbitration/clinvar_by_codon.py -i /data/pathogenic_annotated.vcf.bgz -o /data/pm5" # upon completion, this will generate files in the data directory: # - data/pm5.json - a JSON file containing the PM5 results, one JSON object per line