Commit b9fe6802 authored by josh's avatar josh
Browse files

Added dojo and ninja.

Not sure if these are necessary for shogun or not
parent 4100e3d5
Pipeline #194723 failed with stages
in 42 seconds
......@@ -332,8 +332,10 @@ RUN cd /opt && \
make
# UNDER CONSTRUCTION: Nerd Work Zone <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# --------------------
# SHOGUN
# --------------------
# https://github.com/knights-lab/BURST/releases
# https://github.com/knights-lab/UTree/releases/tag/v2.0c
......@@ -347,11 +349,22 @@ RUN curl -L -s https://github.com/knights-lab/BURST/releases/download/v1.0/burst
chmod 555 burst* && \
mv burst* $MANUAL_BIN
# Not sure if ninja and dojo are necessary for shogun, it mentions them here: <https://github.com/danknights/SHOGUN>
RUN curl -L -s -o ninja.tar.gz https://github.com/knights-lab/NINJA-utils/archive/v0.0.1.tar.gz && \
pip3 install --no-cache-dir ninja.tar.gz && \
rm ninja.tar.gz
RUN curl -L -s -o dojo.tar.gz https://github.com/knights-lab/DOJO/archive/v0.0.1.tar.gz && \
pip3 install --no-cache-dir dojo.tar.gz && \
rm dojo.tar.gz
RUN curl -L -s -o shogun.tar.gz https://github.com/knights-lab/SHOGUN/archive/v1.0.8.tar.gz && \
pip3 install --no-cache-dir shogun.tar.gz && \
rm shogun.tar.gz
# --------------------
# MetaPhlAn
# --------------------
# https://pypi.org/project/MetaPhlAn/
RUN pip3 install --no-cache-dir MetaPhlAn
......@@ -362,7 +375,9 @@ RUN apt-get update && \
bowtie2 \
cutadapt
# --------------------
# kaiju
# --------------------
RUN mkdir kaiju && \
curl -L -s https://github.com/bioinformatics-centre/kaiju/archive/v1.7.4.tar.gz | \
tar -zx -C kaiju --strip-components=1 && \
......
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