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Update pinned software to latest #145

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Update pinned software to latest #145

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96ac3e8
Bump mafft version to v7.520
corneliusroemer May 4, 2023
3a48047
Update IQtree to v2.2.2.4
corneliusroemer May 4, 2023
5c1b62d
Update csvtk to v0.25.0
corneliusroemer May 4, 2023
ccad81d
Update seqkit to v2.4.0
corneliusroemer May 4, 2023
67fde48
Update gofasta to v1.2.0
corneliusroemer May 4, 2023
9bb76df
Update minimamp2 to v2.26
corneliusroemer May 4, 2023
ad77c3a
Update awscli to v1.27.126
corneliusroemer May 4, 2023
21f70b8
Update google-cloud-storage to v2.8.0
corneliusroemer May 4, 2023
59e6ed2
Update epiweeks to v2.2.0
corneliusroemer May 4, 2023
23c3c72
Update snakemake to v7.25.2
corneliusroemer May 4, 2023
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25 changes: 13 additions & 12 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -89,8 +89,9 @@ RUN curl -fsSL https://github.com/vcftools/vcftools/releases/download/v0.1.16/vc
# NOTE: Running this program requires support for emulation on the Docker host
# if the processor architecture is not amd64.
# TODO: Build from source to avoid emulation. Instructions: https://mafft.cbrc.jp/alignment/software/installation_without_root.html
# Last update: 2023-05-03 to v7.520 from v7.475 (~end of 2020)
WORKDIR /download/mafft
RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.475-linux.tgz \
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
Expand All @@ -99,8 +100,9 @@ RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.475-linux.tgz \
# NOTE: Running this program requires support for emulation on the Docker host
# if the processor architecture is not amd64.
# TODO: Build from source to avoid emulation. Instructions: http://www.iqtree.org/doc/Compilation-Guide
# Last update: 2023-05-03 to v2.2.2.4 from v2.1.2 (2020-10-22)
WORKDIR /download/IQ-TREE
RUN curl -fsSL https://github.com/iqtree/iqtree2/releases/download/v2.1.2/iqtree-2.1.2-Linux.tar.gz \
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

Expand All @@ -125,24 +127,24 @@ RUN curl -L -o tsv-utils.tar.gz https://github.com/eBay/tsv-utils/releases/downl
&& rm -f tsv-utils.tar.gz

# Download csvtk
RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.24.0/csvtk_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin
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

# Download seqkit
RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin
RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.4.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin

# Download gofasta (for ncov/Pangolin)
# NOTE: Running this program requires support for emulation on the Docker host
# if the processor architecture is not amd64.
# TODO: Build from source to avoid emulation. Instructions: https://github.com/virus-evolution/gofasta/tree/v0.0.6#installation
RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v0.0.6/gofasta-linux-amd64 \
RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v1.2.0/gofasta-linux-amd64 \
-o /final/bin/gofasta

# Download minimap2 (for ncov/Pangolin)
# NOTE: Running this program requires support for emulation on the Docker host
# if the processor architecture is not amd64.
# TODO: Build from source to avoid emulation. Instructions: https://github.com/lh3/minimap2/tree/v2.24#install
RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 \
| tar xjvpf - --no-same-owner --strip-components=1 -C /final/bin minimap2-2.24_x64-linux/minimap2
RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 \
| tar xjvpf - --no-same-owner --strip-components=1 -C /final/bin minimap2-2.26_x64-linux/minimap2


# 3. Install programs via pip
Expand Down Expand Up @@ -181,17 +183,16 @@ RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
RUN pip3 install envdir==1.0.1

# Install tooling for our AWS Batch builds, which use `aws s3`.
RUN pip3 install awscli==1.18.195
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
RUN pip3 install google-cloud-storage==2.8.0

# Install epiweeks (for ncov)
RUN pip3 install epiweeks==2.1.2
RUN pip3 install epiweeks==2.2.0

# Install Pangolin and PangoLEARN + deps (for ncov)
# The cov-lineages projects aren't available on PyPI, so install via git URLs.
Expand Down