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update vcfbub and vg, and a few other tools #401

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Jun 22, 2024
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update vcfbub and vg, and a few other tools #401

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12 changes: 6 additions & 6 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -95,20 +95,20 @@ RUN cargo --help
RUN git clone https://github.com/marschall-lab/GFAffix.git \
&& cd GFAffix \
&& git pull \
&& git checkout d630eb7d9827340f5f292e57cb3cb5e31e6f86f0 \
&& git checkout a366a94a8d7a2ffbba8978cdbcd071a9b8a03bec \
&& cargo install --force --path . \
&& mv /root/.cargo/bin/gfaffix /usr/local/bin/gfaffix \
&& cd ../ \
&& rm -rf GFAffix

RUN pip install multiqc==1.21
RUN pip install multiqc==1.22.2

RUN wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg && chmod +x vg && mv vg /usr/local/bin/vg
RUN wget https://github.com/vgteam/vg/releases/download/v1.57.0/vg && chmod +x vg && mv vg /usr/local/bin/vg

RUN git clone https://github.com/pangenome/vcfbub \
&& cd vcfbub \
&& git pull \
&& git checkout 26a1f0cb216a423f8547c4ad0e0ce38cb9d324b9 \
&& git checkout db7775f63eab6891acb6000dddfa320146cd7c56 \
&& cargo install --force --path . \
&& mv /root/.cargo/bin/vcfbub /usr/local/bin/vcfbub \
&& cd ../ \
Expand All @@ -126,8 +126,8 @@ RUN git clone --recursive https://github.com/vcflib/vcflib.git \
&& rm -rf vcflib

# Community detection dependencies
RUN pip install igraph==0.10.4
RUN pip install pycairo==1.23.0
RUN pip install igraph==0.11.5
RUN pip install pycairo==1.26.1

# Additional tools
RUN git clone https://github.com/ekg/fastix.git \
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