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Add DIAMOND v2.2.4 #293

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Merged
victorlin merged 1 commit into from
Aug 3, 2026
Merged

Add DIAMOND v2.2.4 #293

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16 changes: 15 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ COPY --from=xx / /
# Add system deps for building
# autoconf, automake: for building VCFtools; may be used by package managers to build from source
# ca-certificates: for secure HTTPS connections
# cmake: for building DIAMOND
# curl: for downloading source files
# git: used in builder-scripts/download-repo
# make: used for building from Makefiles (search for usage); may be used by package managers to build from source
Expand All @@ -34,6 +35,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
automake \
clang \
ca-certificates \
cmake \
curl \
git \
make \
Expand All @@ -56,13 +58,16 @@ ARG TARGETARCH
# https://github.com/tonistiigi/xx#building-on-debian
# binutils, gcc, libc6-dev: for compiling C/C++ programs (TODO: verify)
# g++: for building VCFtools; may be used by package managers to build from source
# libsqlite3-dev, libzstd-dev: for building DIAMOND; may be used by package managers to build from source
# pkg-config: for building VCFtools; may be used by package managers to build from source
# zlib1g-dev: for building VCFtools; may be used by package managers to build from source
# zlib1g-dev: for building DIAMOND, VCFtools; may be used by package managers to build from source
RUN xx-apt-get install -y \
binutils \
gcc \
g++ \
libc6-dev \
libsqlite3-dev \
libzstd-dev \
pkg-config \
zlib1g-dev

Expand Down Expand Up @@ -110,6 +115,15 @@ RUN curl -fsSL https://api.github.com/repos/vcftools/vcftools/tarball/1cab5204eb
&& cp -rp built/bin/* /final/bin \
&& cp -rp built/share/* /final/share

# Build+test DIAMOND
WORKDIR /build/diamond
RUN curl -fsSL https://github.com/bbuchfink/diamond/archive/refs/tags/v2.2.4.tar.gz \
| tar xzvpf - --no-same-owner --strip-components=1 \
&& CC=xx-clang CXX=xx-clang++ cmake -B build -S . \
&& cmake --build build -j$(nproc) \
&& ctest --test-dir build -C Release \
&& cp -p build/diamond /final/bin


# 2. Download pre-built programs

Expand Down
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