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Remove pangoLEARN and its dependencies #237

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Dec 5, 2024
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Remove pangoLEARN and its dependencies #237

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27 changes: 0 additions & 27 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -158,21 +158,6 @@ RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.30.0/csvtk_
# 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

# 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 \
-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


# 3. Add unpinned programs

# Allow caching to be avoided from here on out in this stage by calling
Expand Down Expand Up @@ -268,15 +253,6 @@ RUN pip3 install google-cloud-storage==2.7.0
# Install epiweeks (for ncov)
RUN pip3 install epiweeks==2.1.2

# Install Pangolin and PangoLEARN + deps (for ncov)
# The cov-lineages projects aren't available on PyPI, so install via git URLs.
RUN pip3 install git+https://github.com/cov-lineages/[email protected]
RUN pip3 install git+https://github.com/cov-lineages/pangoLEARN.git@2021-12-06
RUN pip3 install git+https://github.com/cov-lineages/[email protected]
RUN pip3 install git+https://github.com/cov-lineages/[email protected]
RUN pip3 install git+https://github.com/cov-lineages/pango-designation.git@19d9a537b9
RUN pip3 install pysam==0.19.1

# Install pango_aliasor (for forecasts-ncov)
RUN pip3 install pango_aliasor==0.3.0

Expand Down Expand Up @@ -405,12 +381,9 @@ COPY --from=builder-target-platform \
/usr/local/bin/aws \
/usr/local/bin/envdir \
/usr/local/bin/nextstrain \
/usr/local/bin/pangolin \
/usr/local/bin/pangolearn.smk \
/usr/local/bin/pathogen-distance \
/usr/local/bin/pathogen-embed \
/usr/local/bin/pathogen-cluster \
/usr/local/bin/scorpio \
/usr/local/bin/snakemake \
/usr/local/bin/treetime \
/usr/local/bin/
Expand Down
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