diff --git a/docker/Dockerfile.tbprofiler-0.9.8 b/docker/Dockerfile.tbprofiler-0.9.8 new file mode 100644 index 0000000..a6d1671 --- /dev/null +++ b/docker/Dockerfile.tbprofiler-0.9.8 @@ -0,0 +1,46 @@ +FROM mambaorg/micromamba:jammy + +LABEL maintainer="whalleyt@cardiff.ac.uk" \ +about.summary="container for the tb-profiler" + +COPY bin/ /opt/bin/ +COPY resources/tuberculosis.fasta ~/tuberculosis.fasta + +ENV PATH=/opt/bin:$PATH + +ARG TBPROFILER_VER="5.0.1" + +# this version is the shortened commit hash on the `master` branch here https://github.com/jodyphelan/tbdb/ +# commits are found on https://github.com/jodyphelan/tbdb/commits/master +# this was the latest commit as of 2023-10-26 +ARG TBDB_VER="e25540b" + +# Install dependencies via apt-get; cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# install tb-profiler via bioconda; install into 'base' conda env +RUN micromamba install --yes --name base --channel conda-forge --channel bioconda \ + tb-profiler=${TBPROFILER_VER} && \ + micromamba clean --all --yes +# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time +ENV PATH="/opt/conda/bin:${PATH}" + +# Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json +# can also run 'tb-profiler list_db' to find the same version info +# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER} +RUN tb-profiler update_tbdb --commit ${TBDB_VER} + +# hardcode 'base' env bin into PATH, so conda env does not have to be "activated" at run time +ENV PATH="/opt/conda/bin:${PATH}" + +# Version of database can be confirmed at /opt/conda/share/tbprofiler/tbdb.version.json +# can also run 'tb-profiler list_db' to find the same version info +# In 5.0.1 updating_tbdb does not work with tb-profiler update_tbdb --commit ${TBDB_VER} +RUN tb-profiler update_tbdb --commit ${TBDB_VER} + +#pre-add our TB reference +RUN tb-profiler update_tbdb --match_ref ~/tuberculosis.fasta \ No newline at end of file diff --git a/docker/Dockerfile.vcfpredict-0.9.8 b/docker/Dockerfile.vcfpredict-0.9.8 new file mode 100644 index 0000000..068303f --- /dev/null +++ b/docker/Dockerfile.vcfpredict-0.9.8 @@ -0,0 +1,22 @@ +FROM ubuntu:20.04 + +LABEL maintainer="pricea35@cardiff.ac.uk" \ +about.summary="container for the vcf predict workflow" + +ENV PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq" \ +PYTHON="python3 python3-pip python3-dev" + +ENV vcfmix_version=d4693344bf612780723e39ce27c8ae3868f95417 \ + +RUN apt-get update \ +&& DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata \ +&& apt-get install -y $PACKAGES $PYTHON \ +&& apt-get install -y python3-packaging \ +&& git clone https://github.com/JeremyWesthead/VCFMIX.git \ +&& cd VCFMIX \ +&& git checkout ${vcfmix_version} \ +&& pip3 install recursive_diff \ +&& pip3 install awscli \ +&& pip3 install . \ +&& cp -r data /usr/local/lib/python3.8/dist-packages \ +&& cd .. \ No newline at end of file