fix: somalier container (#1487)

* update somalier and dependecies

* update docs

* fix security hotspot

* restrict redirects

* update docs

* changelog

BALSAMIC/containers/msisensorpro/msisensorpro.yaml

@@ -1 +1 @@
-- msisensorpro=1.2.0
+- msisensorpro=1.3.0

BALSAMIC/containers/somalier/Dockerfile

@@ -1,58 +1,75 @@
 FROM alpine:3.11.5
 
-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
+LABEL base.image="alpine:3.11.5" \
+      maintainer="Clinical Genomics" \
+      about.contact="[email protected]" \
+      software="somalier" \
+      software.version="0.2.19" \
+      about.summary="Fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs" \
+      about.home="https://github.com/brentp/somalier" \
+      about.documentation="https://github.com/brentp/somalier/wiki" \
+      about.license="MIT License (MIT)"
 
+ARG nim_version=1.6.20
 ENV CFLAGS="-fPIC -O3"
+ENV HTTPS_METHOD=noredirect
 
-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 upgrade && apk add --no-cache wget git xz bzip2-static musl m4 \
+    autoconf tar xz-dev bzip2-dev build-base libpthread-stubs libzip-dev gfortran \
+    openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static \
+    bash curl-dev clang-static nghttp2-static  zlib-static cmake procps
 
 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 / && \
-    wget -q https://nim-lang.org/download/nim-${nim_version}-linux_x64.tar.xz && \
+    wget --max-redirect=0 -q https://nim-lang.org/download/nim-${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 apk add --no-cache cmake openssl-dev && \
+    wget --max-redirect=0 -q 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 1.18 --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 && \
-    cd somalier && \
-    nimble install -y nimble && \
-    /root/.nimble/bin/nimble install -d -y
+RUN cd / && git clone -b v0.2.19 --depth 5 https://github.com/brentp/somalier.git && \
+    nimble install -y [email protected] && \
+    cd somalier && nimble install -d -y
 
-RUN cd /somalier &&  \
+RUN apk add  --no-cache openblas && \
+    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
+ENV somalier_ancestry_labels=/ancestry_labels-1kg.tsv
+
+RUN rm -rf /var/cache/apk/*
 
 RUN adduser -D defaultuser
 
 USER defaultuser
+

BALSAMIC/containers/somalier/somalier.yaml

@@ -1 +1 @@
-- somalier=0.2.16
+- somalier=0.2.19

CHANGELOG.rst

@@ -52,8 +52,9 @@ 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
-* MSIsensor-pro container https://github.com/Clinical-Genomics/BALSAMIC/pull/
-
+* MSIsensor-pro container and updated msisensor to version 1.3.0  https://github.com/Clinical-Genomics/BALSAMIC/pull/1486
+* Somalier container and updated somalier to version 0.2.19 https://github.com/Clinical-Genomics/BALSAMIC/pull/1487
+
 [15.0.1]
 --------
 

docs/bioinfo_softwares.rst

@@ -86,7 +86,7 @@ msisensor-pro
 ~~~~~~~~~~~~~
 :Source code: `GitHub` `<https://github.com/xjtu-omics/msisensor-pro>`_
 :Article: `Bioinformatics` `<https://doi.org/10.1016/j.gpb.2020.02.001>`_
-:Version: `1.2.0`
+:Version: `1.3.0`
 
 mosdepth
 ~~~~~~~~
@@ -128,7 +128,7 @@ somalier
 ~~~~~~~~
 :Source code: `Github` `<https://github.com/brentp/somalier>`_
 :Article: `Genome Medicine` `<https://doi.org/10.1186/s13073-020-00761-2>`_
-:Version: `0.2.16`
+:Version: `0.2.19`
 
 svdb
 ~~~~

tests/test_data/config.json

@@ -210,7 +210,7 @@
     "svdb": ["2.8.1"],
     "tiddit": ["3.3.2"],
     "vardict": ["2019.06.04"],
-    "somalier": ["0.2.16"],
+    "somalier": ["0.2.19"],
     "delly": ["1.0.3"],
     "manta": ["1.6.0"],
     "bedtools": ["2.30.0"],
@@ -227,7 +227,7 @@
     "ascatNgs": ["4.5.0"],
     "vcf2cytosure": ["0.9.1"],
     "cnvpytor": ["1.2.1"],
-    "msisensorpro": ["1.2.0"]
+    "msisensorpro": ["1.3.0"]
   },
   "panel": {
     "capture_kit": "tests/test_data/references/panel/panel.bed",