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fix: Somalier container #1471

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fix: Somalier container #1471

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fix-somalier-container
ivadym Aug 8, 2024
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changelog
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nim
ivadym Aug 8, 2024
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containersito
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replicate docker
ivadym Aug 9, 2024
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50 changes: 4 additions & 46 deletions BALSAMIC/containers/somalier/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,47 +1,10 @@
FROM alpine:3.11.5
FROM brentp/musl-hts-nim:latest

Check warning on line 1 in BALSAMIC/containers/somalier/Dockerfile

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codefactor.io / CodeFactor

BALSAMIC/containers/somalier/Dockerfile#L1 

Using latest is prone to errors if the image will ever update. Pin the version explicitly to a release tag. (DL3007)

LABEL base.image="alpine:3.11.5"
LABEL about.home="https://github.com/Clinical-Genomics/BALSAMIC"
LABEL about.documentation="https://balsamic.readthedocs.io/"
LABEL about.license="MIT License (MIT)"
LABEL about.description="Bioinformatic analysis pipeline for somatic mutations in cancer"

ARG nim_version=1.6.6

ENV CFLAGS="-fPIC -O3"

RUN apk add --no-cache wget git autoconf tar xz xz-dev bzip2-dev curl curl-dev bash libzip-dev cmake openblas-dev build-base

RUN mkdir -p /usr/local/include && \
git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
cd libdeflate && cmake -B build && cmake --build build && \
cp /libdeflate/build/libdeflate.a /usr/local/lib && cp /libdeflate/libdeflate.h /usr/local/include && \
cd .. && rm -rf libdeflate

RUN cd / && \
wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
tar xf nim-${nim_version}-linux_x64.tar.xz && \
echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bashrc && \
echo 'PATH=/nim-${nim_version}/bin:$PATH' >> ~/.bash_profile && \
echo 'PATH=/nim-${nim_version}/bin:$PATH' >> /etc/environment && \
rm -f nim-${nim_version}-linux_x64.tar.xz

ENV PATH=/nim-${nim_version}/bin/:$PATH

RUN cd / && \
git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
cd htslib && autoheader && autoconf && \
./configure --enable-s3 --enable-gcs --enable-libcurl --with-libdeflate && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../ && \
git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/bcftools && \
cd bcftools && autoheader && autoconf && \
./configure --enable-s3 --enable-libcurl --with-libdeflate && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../ && rm -rf htslib bcftools
# for nextflow
RUN apk add bash procps

Check notice on line 4 in BALSAMIC/containers/somalier/Dockerfile

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codefactor.io / CodeFactor

BALSAMIC/containers/somalier/Dockerfile#L4 

Use the `--no-cache` switch to avoid the need to use `--update` and remove `/var/cache/apk/*` when done installing packages. (DL3019)

RUN cd / && \
git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
git clone -b master --depth 5 https://github.com/brentp/somalier.git && \
cd somalier && \
nimble install -y nimble && \
/root/.nimble/bin/nimble install -d -y
Expand All @@ -52,8 +15,3 @@
rm -rf /somalier && somalier --help

ENV somalier_ancestry_labels /ancestry_labels-1kg.tsv

RUN adduser -D defaultuser

USER defaultuser

1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -26,6 +26,7 @@ Fixed:
* MSI table https://github.com/Clinical-Genomics/BALSAMIC/pull/1459
* Pin numpy version in CNVkit container https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
* CNVkit incorrect version in the documentation https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
* Somalier container https://github.com/Clinical-Genomics/BALSAMIC/pull/1471

[15.0.1]
--------
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