From b60448a2c4cf7b09786c1b5c16a0c26bd8715613 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Wed, 4 Sep 2024 14:21:16 +0000 Subject: [PATCH] first attempt of dockerfile for ntm-profiler --- docker/Dockerfile.ntmprofiler-0.9.9 | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 docker/Dockerfile.ntmprofiler-0.9.9 diff --git a/docker/Dockerfile.ntmprofiler-0.9.9 b/docker/Dockerfile.ntmprofiler-0.9.9 new file mode 100644 index 0000000..8d1e343 --- /dev/null +++ b/docker/Dockerfile.ntmprofiler-0.9.9 @@ -0,0 +1,28 @@ +FROM ubuntu:focal + +ENV pathogenprofiler_version="3b4c6e2ffba8f7a44d12cc2ed4369ee635464093" +ENV ntmprofiler_version="2e4116bff2c09461b2d452f4075c6589e0a66965" +ENV ntmdb_version="93c979b4c3825c591e5bceb55f86538e10d556d2" + +ARG PATHOGEN_PROFILER_VERSION="3b4c6e2ffba8f7a44d12cc2ed4369ee635464093" +ARG NTM_PROFILER_VERSION="2e4116bff2c09461b2d452f4075c6589e0a66965" +ARG NTMDB_VERSION="93c979b4c3825c591e5bceb55f86538e10d556d2" + +#python packages +ENV PACKAGES="procps curl wget git build-essential libhdf5-dev libffi-dev r-base-core jq" \ + PYTHON="python3.9 python3-pip python3-dev" + +#apt-get python stuff +RUN apt-get update +RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata +RUN apt-get install -y $PACKAGES +RUN apt-get install -y $PYTHON +RUN apt-get install -y python3-packaging + +#use pip to install ntm stuff +RUN pip install pysam joblib tqdm pydantic +RUN pip install git+https://github.com/jodyphelan/pathogen-profiler.git@${PATHOGEN_PROFILER_VERSION} +RUN pip install git+https://github.com/jodyphelan/ntm-profiler.git@${NTM_PROFILER_VERSION} + +#update DB to our commit +RUN ntm-profiler update_db --commit ${NTMDB_VERSION}