Commit 9c2fdcbd authored by josh's avatar josh
Browse files

try trimmomatic.py from bioconda for shi7 work

parent bbbfea44
Pipeline #211366 passed with stages
in 1 minute and 7 seconds
......@@ -398,6 +398,11 @@ RUN mkdir kaiju && \
RUN curl -L -s -o shi7.tar.gz https://github.com/knights-lab/shi7/archive/refs/tags/v1.0.2.tar.gz && \
pip3 install --no-cache-dir shi7.tar.gz && \
rm shi7.tar.gz
# Fiddle with trimmomatic so shi7 is happy
RUN curl -L -s -o /opt/bin/trimmomatic https://raw.githubusercontent.com/bioconda/bioconda-recipes/master/recipes/trimmomatic/trimmomatic.py && \
chmod 555 /opt/bin/trimmomatic && \
ln -s /usr/share/java/trimmomatic-0.39.jar /opt/bin/trimmomatic.jar
# --------------------
# Final apt cleanup
......
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