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Add Nextclade v3 alpha; remove Nextclade v1 #195

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merged 4 commits into from
Nov 30, 2023
Merged

Add Nextclade v3 alpha; remove Nextclade v1 #195

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f49abf9
Remove Nextclade v1
victorlin Nov 29, 2023
5e3962f
Pin Nextclade v2
victorlin Nov 29, 2023
1f1922e
Move curl -o paths to its own line
victorlin Nov 29, 2023
81148f4
Add Nextclade v3
victorlin Nov 29, 2023
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52 changes: 25 additions & 27 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -131,17 +131,20 @@ RUN curl -fsSL https://github.com/iqtree/iqtree2/releases/download/v2.1.2/iqtree
| tar xzvpf - --no-same-owner --strip-components=1 \
&& mv bin/iqtree2 /final/bin/iqtree

# Download Nextalign v1
# 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. Example: https://github.com/nextstrain/nextclade/blob/1.11.0/.circleci/config.yml#L183-L223
RUN curl -fsSL -o /final/bin/nextalign1 https://github.com/nextstrain/nextclade/releases/download/1.11.0/nextalign-Linux-x86_64
# Add helper scripts
COPY builder-scripts/ /builder-scripts/

# Download Nextclade v1
# 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. Example: https://github.com/nextstrain/nextclade/blob/1.11.0/.circleci/config.yml#L183-L223
RUN curl -fsSL -o /final/bin/nextclade1 https://github.com/nextstrain/nextclade/releases/download/1.11.0/nextclade-Linux-x86_64
# Download Nextalign v2
# Set default Nextalign version to 2
RUN curl -fsSL https://github.com/nextstrain/nextclade/releases/download/2.14.0/nextalign-$(/builder-scripts/target-triple) \
-o /final/bin/nextalign2 \
&& ln -sv nextalign2 /final/bin/nextalign

# Download Nextclade v2
# Set default Nextclade version to 2
RUN curl -fsSL https://github.com/nextstrain/nextclade/releases/download/2.14.0/nextclade-$(/builder-scripts/target-triple) \
-o /final/bin/nextclade2 \
&& ln -sv nextclade2 /final/bin/nextclade

# Download tsv-utils
# NOTE: Running this program requires support for emulation on the Docker host
Expand Down Expand Up @@ -180,21 +183,14 @@ RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-
# devel/validate-platforms.
ARG CACHE_DATE

# Add helper scripts
COPY builder-scripts/ /builder-scripts/

# Nextclade/Nextalign v2 are downloaded directly but using the latest version,
# so they belong after CACHE_DATE (unlike Nextclade/Nextalign v1).

# 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

# 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-$(/builder-scripts/target-triple) \
&& ln -sv nextclade2 /final/bin/nextclade
# Download Nextclade v3
# Note: Before v3 there used to be separate binaries for Nextclade and
# Nextalign. Since v3 there is only Nextclade, which can do both.
# TODO: After Nextclade 3 is released, update the URL to download the latest
# version instead of hardcoded.
# TODO: At some point, update the v2 binary symlinks to use Nextclade v3.
RUN curl -fsSL https://github.com/nextstrain/nextclade/releases/download/3.0.0-alpha.0/nextclade-$(/builder-scripts/target-triple) \
-o /final/bin/nextclade3

# Auspice
# Building auspice means we can run it without hot-reloading, which is
Expand All @@ -220,8 +216,10 @@ RUN /builder-scripts/download-repo https://github.com/nextstrain/auspice release
&& npm install --omit dev && npm link

# Add NCBI Datasets command line tools for access to NCBI Datsets Virus Data Packages
RUN curl -fsSL -o /final/bin/datasets https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-${TARGETARCH}/datasets
RUN curl -fsSL -o /final/bin/dataformat https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-${TARGETARCH}/dataformat
RUN curl -fsSL https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-${TARGETARCH}/datasets \
-o /final/bin/datasets
RUN curl -fsSL https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-${TARGETARCH}/dataformat \
-o /final/bin/dataformat

# ———————————————————————————————————————————————————————————————————— #

Expand Down