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Precompile quast dependencies #38

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Oct 8, 2024
Merged

Precompile quast dependencies #38

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13 changes: 12 additions & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@ MAINTAINER KBase Developer
# Insert apt-get instructions here to install
# any required dependencies for your module.

RUN apt update && apt install -y g++ nano tree
# libz is for Minimap2 in Quast
RUN apt update && apt install -y g++ nano tree wget libz-dev

RUN python -m pip install --upgrade pip \
&& pip install \
Expand All @@ -18,6 +19,16 @@ RUN python -m pip install --upgrade pip \

# Genemark is not open source for non-academic use, and so can't be used in KBase

# Precompile dependencies vs compiling at first use
# In particular, this allows the container to run @ NERSC
RUN mkdir /quasttemp \
&& cd /quasttemp \
&& wget quast.sf.net/test_data.tar.gz \
&& tar xzf test_data.tar.gz \
&& quast.py --test --debug \
&& cd - \
&& rm -r /quasttemp

# -----------------------------------------

COPY ./ /kb/module
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