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bump alpine to 3.15 and fix htslib dependency
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htslib 1.10 is required for current cyvcf2
we install cython before we can install cyvcf2
blankdots committed Dec 31, 2021
1 parent aa4044f commit f0bd1ec
Showing 1 changed file with 9 additions and 3 deletions.
12 changes: 9 additions & 3 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -1,22 +1,28 @@
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/*

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

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