From f0bd1ec175588cfc660f33d2b4b94600c2641c8b Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Fri, 31 Dec 2021 15:47:58 +0200 Subject: [PATCH] bump alpine to 3.15 and fix htslib dependency htslib 1.10 is required for current cyvcf2 we install cython before we can install cyvcf2 --- Dockerfile | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index dd309e1f..640ace57 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,8 +1,8 @@ -FROM python:3.8-alpine3.13 as BUILD +FROM python:3.8-alpine3.15 as BUILD RUN apk add --update \ && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\ - && apk add --no-cache libressl-dev libffi-dev autoconf bzip2-dev xz-dev\ + && apk add --no-cache openssl-dev libffi-dev autoconf bzip2-dev xz-dev\ && apk add --no-cache python3-dev rust cargo \ && rm -rf /var/cache/apk/* @@ -10,13 +10,19 @@ COPY requirements.txt /root/beacon/requirements.txt COPY setup.py /root/beacon/setup.py COPY beacon_api /root/beacon/beacon_api +RUN git clone --depth 1 --branch 1.10 git://github.com/samtools/htslib.git && \ + cd htslib && \ + make && \ + make install + ENV CYTHONIZE=1 RUN pip install --upgrade pip && \ + pip install Cython==0.29.26 && \ pip install -r /root/beacon/requirements.txt && \ pip install /root/beacon -FROM python:3.8-alpine3.13 +FROM python:3.8-alpine3.15 RUN apk add --no-cache --update bash