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fix: Somalier container #1471

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fix: Somalier container #1471

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2282c1e
fix-somalier-container
ivadym Aug 8, 2024
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changelog
ivadym Aug 8, 2024
ea88d75
nim
ivadym Aug 8, 2024
12be1d8
containersito
ivadym Aug 8, 2024
e86a313
nim
ivadym Aug 8, 2024
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replicate docker
ivadym Aug 9, 2024
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58 changes: 42 additions & 16 deletions BALSAMIC/containers/somalier/Dockerfile
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Expand Up @@ -10,12 +10,13 @@

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 apk update && apk upgrade && apk add wget git xz bzip2-static musl m4 autoconf tar xz-dev bzip2-dev build-base libpthread-stubs libzip-dev gfortran \

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codefactor.io / CodeFactor

BALSAMIC/containers/somalier/Dockerfile#L13 

Use the `--no-cache` switch to avoid the need to use `--update` and remove `/var/cache/apk/*` when done installing packages. (DL3019)
openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static bash procps curl-dev clang-static nghttp2-static zlib-static cmake

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Arguments in long RUN instructions should be sorted Low

Sort these package names alphanumerically. See more on SonarCloud

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 && \
git clone -b v1.18 --depth 1 https://github.com/ebiggers/libdeflate.git && \
cd libdeflate && cmake -B build && cmake --build build && cmake --install build && \
ln -s /usr/local/lib64/* /usr/local/lib && \
cd .. && rm -rf libdeflate

RUN cd / && \
Expand All @@ -26,34 +27,59 @@
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 apk add cmake openssl-dev && \

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BALSAMIC/containers/somalier/Dockerfile#L30 

Avoid use of wget without progress bar. Use `wget --progress=dot:giga <url>`. Or consider using `-q` or `-nv` (shorthands for `--quiet` or `--no-verbose`). (DL3047)

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BALSAMIC/containers/somalier/Dockerfile#L30 

Use the `--no-cache` switch to avoid the need to use `--update` and remove `/var/cache/apk/*` when done installing packages. (DL3019)
wget https://libzip.org/download/libzip-1.6.1.tar.gz && \
tar xzvf libzip-1.6.1.tar.gz && \
cd libzip-1.6.1 && \
mkdir build && cd build && \
cmake -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/ ../ && \
make -j4 CFLAGS="-fPIC -O3" install && \
cd ../../ && rm -rf libzip-1.6.1*

RUN cd / && \
git clone --depth 1 -b 1.15 --recursive https://github.com/samtools/htslib && \
ENV PATH=:/root/.nimble/bin:/nim-${nim_version}/bin/:$PATH

RUN git clone --depth 1 -b 1.19.1 --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 && \
git clone --depth 1 -b 1.18 --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

RUN cd / && \
git clone -b v0.2.16 --depth 1 https://github.com/brentp/somalier.git && \
ENV RUSTFLAGS=-Ctarget-feature=-crt-static

RUN sh -c 'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y' \
&& ~/.cargo/bin/rustup target add x86_64-unknown-linux-musl \
&& git clone https://github.com/38/d4-format \
&& cd d4-format \
&& ln -s /usr/bin/gcc /usr/bin/musl-gcc \
&& ~/.cargo/bin/cargo build --package=d4binding --release && cd .. \
&& install -m 644 d4-format/target/release/libd4binding.a /usr/lib \
&& install -m 644 d4-format/d4binding/include/d4.h /usr/include \
&& rm -rf d4-format/target/ \
&& rm -rf /root/.rustup/ \
&& rm -rf ~/.cargo

ADD . /src/
Fixed Show fixed Hide fixed
RUN cat /src/docker/docker.nim.cfg >> /nim-${nim_version}/config/nim.cfg && \
cd /src/ && nimble install -y && \
nimble install -y c2nim docopt && \
nimble install -y websocket@#head && \
nim c -o:/usr/local/bin/nsb /src/docker/nsb.nim && \
rm -rf /src/

RUN cd / && \
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

RUN cd /somalier && \
RUN cd /somalier && \
nim c -d:danger -d:nsb_static -d:release -d:openmp -d:blas=openblas -d:lapack=openblas -o:/usr/bin/somalier src/somalier && \
cp scripts/ancestry-labels-1kg.tsv / && \
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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