requirements.txt

# WORKDIR /tmp
# RUN DEBIAN_FRONTEND=noninteractive \

RUN  apt-get update \
	&& apt-get install -y --no-install-recommends \
		python3-pip \
		git \
		curl \
		wget \
		bzip2 \
		make \
		cmake \
		zlib1g-dev \
		python3-all-dev \
		libhdf5-dev \
		libatlas-base-dev \
		libopenblas-base \
		libopenblas-dev \
		libbz2-dev \
		liblzma-dev \
		libffi-dev  \
		python-virtualenv \
	&& curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh \
	&& apt-get install default-jre -y --no-install-recommends \
	&& wget https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar \
	&& cp pilon-1.23.jar /usr/local/bin \
	&& wget https://github.com/shenwei356/seqkit/releases/download/v0.11.0/seqkit_linux_amd64.tar.gz \
	&& tar -zxf seqkit_linux_amd64.tar.gz \
	&& cp seqkit /usr/local/bin \
	&& git clone https://github.com/lh3/minimap2 \
	&& pip3 install git+https://github.com/rrwick/Porechop \
	&& pip3 install pomoxis \
	&& virtualenv pomoxis --python=python3 --prompt "(pomoxis) " 


### Dockerfile used above	; below is later interactive

cd minimap2 
make
cp minimap2 /usr/local/bin 
bash Anaconda3-2019.03-Linux-x86_64.sh \ # -yes \r \r -y

# exit bash to activate
conda install -c bioconda nanoplot -y \
conda install -c bioconda filtlong -y \
source ~/.bashrc \
conda create -n nanopolish -c bioconda -c conda-forge nanopolish -y
conda install -c conda-forge -c bioconda -c defaults canu -y \
 
# Pilon
java -Xmx16G  -jar /usr/local/bin/pilon-1.23.jar --help

# Pomoxis
 . pomoxis/bin/activate
deactivate 

### Maybe not needed
#	&& sudo add-apt-repository ppa:deadsnakes/ppa	\
-		python3.7 \
-		virtualenv \