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update wfmash/seqwish/smoothxg/odgi #386

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Apr 7, 2024
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update wfmash/seqwish/smoothxg/odgi #386

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6 changes: 3 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.
RUN git clone --recursive https://github.com/waveygang/wfmash \
&& cd wfmash \
&& git pull \
&& git checkout e7850f9e9ba743a350b36b5e51ae8c414fba717d \
&& git checkout d7b696087f634f25e4b3de7dd521e1c4bfa3cf0e \
&& git submodule update --init --recursive \
&& sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \
&& cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
Expand All @@ -66,7 +66,7 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \
RUN git clone --recursive https://github.com/ekg/seqwish \
&& cd seqwish \
&& git pull \
&& git checkout f44b402f0c2e02988d431d9b2e5eba9727cf93a9 \
&& git checkout 75e807c7e3e92c84068cd3c2c7394eb313732a0a \
&& git submodule update --init --recursive \
&& cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
&& cp bin/seqwish /usr/local/bin/seqwish \
Expand All @@ -76,7 +76,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
RUN git clone --recursive https://github.com/pangenome/smoothxg \
&& cd smoothxg \
&& git pull \
&& git checkout 4c269081faf86302e22f0271931b2d862277d3fa \
&& git checkout c216a84c51e8fa462aa0e26e56f08e4580d5c69c \
&& git submodule update --init --recursive \
&& sed -i 's/-msse4.1/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
&& sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
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