From b2d513596dc2270fa3b446a14ae127f93137b797 Mon Sep 17 00:00:00 2001 From: Tom Whalley Date: Wed, 4 Sep 2024 15:19:37 +0000 Subject: [PATCH] python3.12 --- docker/Dockerfile.ntmprofiler-0.9.9 | 26 ++++++++++++++++---------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/docker/Dockerfile.ntmprofiler-0.9.9 b/docker/Dockerfile.ntmprofiler-0.9.9 index 8d1e343..e2faef9 100644 --- a/docker/Dockerfile.ntmprofiler-0.9.9 +++ b/docker/Dockerfile.ntmprofiler-0.9.9 @@ -1,4 +1,4 @@ -FROM ubuntu:focal +FROM ubuntu:jammy ENV pathogenprofiler_version="3b4c6e2ffba8f7a44d12cc2ed4369ee635464093" ENV ntmprofiler_version="2e4116bff2c09461b2d452f4075c6589e0a66965" @@ -10,19 +10,25 @@ 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" + PYTHON="python3.12 python3-pip python3-dev python3-packaging" #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 +RUN apt-get update && \ + DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install \ + tzdata software-properties-common && \ + add-apt-repository ppa:deadsnakes/ppa && \ + apt install -y $PACKAGES $PYTHON && \ + apt remove -y python3.8 && \ + apt install -y python3.12-distutils python3.12-venv + +#reinstall pip +RUN python3.12 -m ensurepip --upgrade +RUN python3.12 -m pip install --upgrade setuptools #use pip to install ntm stuff -RUN pip install pysam joblib tqdm pydantic -RUN pip install git+https://github.com/jodyphelan/pathogen-profiler.git@${PATHOGEN_PROFILER_VERSION} -RUN pip install git+https://github.com/jodyphelan/ntm-profiler.git@${NTM_PROFILER_VERSION} +RUN python3.12 -m pip install pysam joblib tqdm pydantic jinja2 rich-argparse packaging +RUN python3.12 -m pip install git+https://github.com/jodyphelan/pathogen-profiler.git@${PATHOGEN_PROFILER_VERSION} +RUN python3.12 -m 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}