avsastry/fasterq-dump repository overview

FROM ubuntu:18.04

# Metadata
MAINTAINER Anand Sastry <[email protected]>

# Set noninteractive mode
ENV DEBIAN_FRONTEND noninteractive

# Install pigz and sra-toolbox
USER root
RUN apt-get update && apt-get install -y procps pigz wget libxml-libxml-perl
RUN wget -q http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6/sratoolkit.2.9.6-ubuntu64.tar.gz -O /tmp/sratoolkit.tar.gz && tar zxf /tmp/sratoolkit.tar.gz -C /opt/ && rm /tmp/sratoolkit.tar.gz

RUN mkdir //ncbi && mkdir //ncbi/public && mkdir //ncbi/public/sra && mkdir //ncbi/public/refseq && chmod -R 777 //ncbi

ENV PATH="/opt/sratoolkit.2.9.6-ubuntu64/bin/:${PATH}"