Commit 942d947e authored by josh's avatar josh
Browse files

trying to install all of Eva's requests

parent 76889c79
......@@ -2,7 +2,7 @@
#
# VERSION 1.1
FROM ubuntu:18.04
FROM ubuntu:20.04
MAINTAINER Mark McCahill "mark.mccahill@duke.edu"
ENV DEBIAN_FRONTEND noninteractive
......@@ -166,7 +166,7 @@ RUN apt-get update && \
libgdal-dev \
build-essential \
python-dev \
python-pip \
python3-pip \
python-numpy \
python-matplotlib \
python-pandas \
......@@ -233,7 +233,7 @@ RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
rm -rf ${TRANSABYSS_VERSION}.tar.gz transabyss-${TRANSABYSS_VERSION}
# DukeDSClient
RUN pip install DukeDSClient multiqc
RUN pip3 install --no-cache-dir DukeDSClient multiqc
# Install FastTree and FastTreeMP
RUN mkdir -p $MANUAL_BIN && \
......@@ -343,6 +343,26 @@ RUN cd /opt && \
# UNDER CONSTRUCTION: Nerd Work Zone <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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
RUN pip3 install --no-cache-dir MetaPhlAn
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
kraken2 \
bowtie2
RUN mkdir kaiju && \
curl -L -s kaiju.tar.gz https://github.com/bioinformatics-centre/kaiju/archive/v1.7.4.tar.gz | \
tar -zx -C kaiju --strip-components=1 && \
cd kaiju/src && \
make && \
mv kaiju/bin/* $MANUAL_BIN && \
rm -rf kaiju
RUN apt-get clean && \
rm -rf /var/lib/apt/lists/*
......
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