Update snakemake to v7.25.2

Author: corneliusroemer

Dockerfile

@@ -21,21 +21,21 @@ SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]
 # zlib1g-dev: for building VCFtools and pyfastx; may be used by package managers to build from source
 # nodejs: for installing Auspice
 RUN apt-get update && apt-get install -y --no-install-recommends \
-        autoconf \
-        automake \
-        build-essential \
-        ca-certificates \
-        curl \
-        git \
-        jq \
-        libsqlite3-dev \
-        pkg-config \
-        zlib1g-dev
+  autoconf \
+  automake \
+  build-essential \
+  ca-certificates \
+  curl \
+  git \
+  jq \
+  libsqlite3-dev \
+  pkg-config \
+  zlib1g-dev
 
 # Install a specific Node.js version
 # https://github.com/nodesource/distributions/blob/0d81da75/README.md#installation-instructions
 RUN curl -fsSL https://deb.nodesource.com/setup_14.x | bash - \
- && apt-get update && apt-get install -y nodejs
+  && apt-get update && apt-get install -y nodejs
 
 # Used for platform-specific instructions
 ARG TARGETPLATFORM
@@ -70,17 +70,17 @@ RUN curl -fsSL https://api.github.com/repos/nextstrain/standard-RAxML/tarball/46
 WORKDIR /build/FastTree
 RUN curl -fsSL https://api.github.com/repos/tsibley/FastTree/tarball/50c5b098ea085b46de30bfc29da5e3f113353e6f \
   | tar xzvpf - --no-same-owner --strip-components=1 \
- && make FastTreeDblMP \
- && cp -p FastTreeDblMP /final/bin
+  && make FastTreeDblMP \
+  && cp -p FastTreeDblMP /final/bin
 
 # Build vcftools
 WORKDIR /build/vcftools
 RUN curl -fsSL https://github.com/vcftools/vcftools/releases/download/v0.1.16/vcftools-0.1.16.tar.gz \
   | tar xzvpf - --no-same-owner --strip-components=2 \
- && ./configure --prefix=$PWD/built \
- && make && make install \
- && cp -rp built/bin/*    /final/bin \
- && cp -rp built/share/*  /final/share
+  && ./configure --prefix=$PWD/built \
+  && make && make install \
+  && cp -rp built/bin/*    /final/bin \
+  && cp -rp built/share/*  /final/share
 
 
 # 2. Download pre-built programs
@@ -93,8 +93,8 @@ RUN curl -fsSL https://github.com/vcftools/vcftools/releases/download/v0.1.16/vc
 WORKDIR /download/mafft
 RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz \
   | tar xzvpf - --no-same-owner --strip-components=2 mafft-linux64/mafftdir/ \
- && cp -p bin/*     /final/bin \
- && cp -p libexec/* /final/libexec
+  && cp -p bin/*     /final/bin \
+  && cp -p libexec/* /final/libexec
 
 # Download IQ-TREE
 # NOTE: Running this program requires support for emulation on the Docker host
@@ -104,7 +104,7 @@ RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz \
 WORKDIR /download/IQ-TREE
 RUN curl -fsSL https://github.com/iqtree/iqtree2/releases/download/v2.2.2.4/iqtree-2.2.2.4-Linux.tar.gz \
   | tar xzvpf - --no-same-owner --strip-components=1 \
- && mv bin/iqtree2 /final/bin/iqtree
+  && mv bin/iqtree2 /final/bin/iqtree
 
 # Download Nextalign v1
 # NOTE: Running this program requires support for emulation on the Docker host
@@ -123,8 +123,8 @@ RUN curl -fsSL -o /final/bin/nextclade1 https://github.com/nextstrain/nextclade/
 # if the processor architecture is not amd64.
 # TODO: Build from source to avoid emulation. Instructions: https://github.com/eBay/tsv-utils/tree/v2.2.0#build-from-source-files
 RUN curl -L -o tsv-utils.tar.gz https://github.com/eBay/tsv-utils/releases/download/v2.2.0/tsv-utils-v2.2.0_linux-x86_64_ldc2.tar.gz \
- && tar -x --no-same-owner -v -C /final/bin -z --strip-components 2 --wildcards -f tsv-utils.tar.gz "*/bin/*" \
- && rm -f tsv-utils.tar.gz
+  && tar -x --no-same-owner -v -C /final/bin -z --strip-components 2 --wildcards -f tsv-utils.tar.gz "*/bin/*" \
+  && rm -f tsv-utils.tar.gz
 
 # Download csvtk
 RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.25.0/csvtk_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin
@@ -162,22 +162,22 @@ RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-
 # ¹ https://cvxopt.org/install/#building-and-installing-from-source
 # ² https://github.com/cvxopt/cvxopt/issues/125#issuecomment-407396491
 RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
-      apt-get update && apt-get install -y --no-install-recommends \
-          libopenblas-dev \
-          libsuitesparse-dev \
-   && CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse \
-      pip3 install cvxopt \
-      ; \
-    fi
+  apt-get update && apt-get install -y --no-install-recommends \
+  libopenblas-dev \
+  libsuitesparse-dev \
+  && CVXOPT_SUITESPARSE_INC_DIR=/usr/include/suitesparse \
+  pip3 install cvxopt \
+  ; \
+  fi
 
 # Install jaxlib on linux/arm64
 # jaxlib, an evofr dependency, does not have official pre-built binaries for
 # linux/arm64. A GitHub user has provided them in a fork repo.
 # https://github.com/google/jax/issues/7097#issuecomment-1110730040
 RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
-      pip3 install https://github.com/yoziru/jax/releases/download/jaxlib-v0.4.6/jaxlib-0.4.6-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl \
-      ; \
-    fi
+  pip3 install https://github.com/yoziru/jax/releases/download/jaxlib-v0.4.6/jaxlib-0.4.6-cp310-cp310-manylinux2014_aarch64.manylinux_2_17_aarch64.whl \
+  ; \
+  fi
 
 # Install envdir, which is used by pathogen builds
 RUN pip3 install envdir==1.0.1
@@ -186,8 +186,7 @@ RUN pip3 install envdir==1.0.1
 RUN pip3 install awscli==1.27.126
 
 # Install Snakemake and related optional dependencies.
-# Pinned to 7.24.1 for stability (2023-03-13)
-RUN pip3 install snakemake==7.24.1
+RUN pip3 install snakemake==7.25.2
 # Google Cloud Storage package is required for Snakemake to fetch remote files
 # from Google Storage URIs.
 RUN pip3 install google-cloud-storage==2.7.0
@@ -225,17 +224,17 @@ COPY builder-scripts/ /builder-scripts/
 # Download Nextalign v2
 # Set default Nextalign version to 2
 RUN curl -fsSL -o /final/bin/nextalign2 https://github.com/nextstrain/nextclade/releases/latest/download/nextalign-$(/builder-scripts/target-triple) \
- && ln -sv nextalign2 /final/bin/nextalign
+  && ln -sv nextalign2 /final/bin/nextalign
 
 # Download Nextclade v2
 # Set default Nextclade version to 2
 RUN curl -fsSL -o /final/bin/nextclade2 https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-$(/builder-scripts/target-triple) \
- && ln -sv nextclade2 /final/bin/nextclade
+  && ln -sv nextclade2 /final/bin/nextclade
 
 # Fauna
 WORKDIR /nextstrain/fauna
 RUN /builder-scripts/download-repo https://github.com/nextstrain/fauna master . \
- && pip3 install --requirement=requirements.txt
+  && pip3 install --requirement=requirements.txt
 
 # Add Treetime
 RUN pip3 install phylo-treetime
@@ -246,7 +245,7 @@ RUN pip3 install phylo-treetime
 # accessible and importable.
 WORKDIR /nextstrain/augur
 RUN /builder-scripts/download-repo https://github.com/nextstrain/augur "$(/builder-scripts/latest-augur-release-tag)" . \
- && pip3 install --editable .
+  && pip3 install --editable .
 
 # Auspice
 # Install Node deps, build Auspice, and link it into the global search path.  A
@@ -257,7 +256,7 @@ RUN /builder-scripts/download-repo https://github.com/nextstrain/augur "$(/build
 # used for the same reasons described above.
 WORKDIR /nextstrain/auspice
 RUN /builder-scripts/download-repo https://github.com/nextstrain/auspice release . \
- && npm update && npm install && npm run build && npm link
+  && npm update && npm install && npm run build && npm link
 
 # Add evofr for forecasting
 RUN pip3 install evofr
@@ -288,28 +287,28 @@ SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]
 # zlib1g: for pyfastx (for Augur)
 # nodejs: for running Auspice
 RUN apt-get update && apt-get install -y --no-install-recommends \
-        bzip2 \
-        ca-certificates \
-        curl \
-        dos2unix \
-        gzip \
-        jq \
-        less \
-        libgomp1 \
-        libsqlite3-0 \
-        perl \
-        ruby \
-        util-linux \
-        wget \
-        xz-utils \
-        zip unzip \
-        zlib1g \
-        zstd
+  bzip2 \
+  ca-certificates \
+  curl \
+  dos2unix \
+  gzip \
+  jq \
+  less \
+  libgomp1 \
+  libsqlite3-0 \
+  perl \
+  ruby \
+  util-linux \
+  wget \
+  xz-utils \
+  zip unzip \
+  zlib1g \
+  zstd
 
 # Install a specific Node.js version
 # https://github.com/nodesource/distributions/blob/0d81da75/README.md#installation-instructions
 RUN curl -fsSL https://deb.nodesource.com/setup_14.x | bash - \
- && apt-get update && apt-get install -y nodejs
+  && apt-get update && apt-get install -y nodejs
 
 # Configure bash for interactive usage
 COPY bashrc /etc/bash.bashrc
@@ -338,16 +337,16 @@ COPY --from=builder /usr/local/lib/python3.10/site-packages/ /usr/local/lib/pyth
 # troublesome or excessive.
 #   -trs, 15 June 2018
 COPY --from=builder \
-    /usr/local/bin/augur \
-    /usr/local/bin/aws \
-    /usr/local/bin/envdir \
-    /usr/local/bin/nextstrain \
-    /usr/local/bin/pangolin \
-    /usr/local/bin/pangolearn.smk \
-    /usr/local/bin/scorpio \
-    /usr/local/bin/snakemake \
-    /usr/local/bin/treetime \
-    /usr/local/bin/
+  /usr/local/bin/augur \
+  /usr/local/bin/aws \
+  /usr/local/bin/envdir \
+  /usr/local/bin/nextstrain \
+  /usr/local/bin/pangolin \
+  /usr/local/bin/pangolearn.smk \
+  /usr/local/bin/scorpio \
+  /usr/local/bin/snakemake \
+  /usr/local/bin/treetime \
+  /usr/local/bin/
 
 # Add installed Node libs
 COPY --from=builder /usr/lib/node_modules/ /usr/lib/node_modules/
@@ -373,11 +372,11 @@ ENV HOME=/nextstrain
 
 # Setup a non-root user for optional use
 RUN useradd nextstrain \
-    --system \
-    --user-group \
-    --shell /bin/bash \
-    --home-dir /nextstrain \
-    --no-log-init
+  --system \
+  --user-group \
+  --shell /bin/bash \
+  --home-dir /nextstrain \
+  --no-log-init
 
 # The host should bind mount the pathogen build dir into /nextstrain/build.
 WORKDIR /nextstrain/build