IDP/Dockerfile at master · jason-weirather/IDP · GitHub

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from vacation/lsc:2.0.1

# Based on the short read correction software LSC because of
#    shared dependencies
# Highly recommend using short read correction software LoRDEC
#    with the IDP because it is much faster

RUN apt-get update \
    && apt-get upgrade -y \
    && apt-get install -y \
               wget \
               python-scipy \
               zip

# Include LoRDEC - it has a boutique open source license I can only find
#    in their full source which is here:
#    http://www.atgc-montpellier.fr/download/sources/lordec/LoRDEC-0.6.tar.gz
RUN cd /Source \
    && wget http://gatb-tools.gforge.inria.fr/versions/bin/LoRDEC-0.6-Linux.tar.gz \
    && tar -xzf LoRDEC-0.6-Linux.tar.gz \
    && rm LoRDEC-0.6-Linux.tar.gz \
    && cp LoRDEC-0.6-Linux/bin/* /usr/local/bin/ \
    && rm -r LoRDEC-0.6-Linux/

# Include GMAP
#    note that GMAP is not open source to everyone. please abide by the license.
RUN cd /Source \
    && wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-09-11.tar.gz \
    && tar -xzf gmap-gsnap-2017-09-11.tar.gz \
    && rm gmap-gsnap-2017-09-11.tar.gz \
    && cd gmap-2017-09-11 \
    && ./configure \
    && make \
    && make install \
    && cd /Source \
    && rm -r gmap-2017-09-11

## Include IDP
RUN cd /Source \
    && git clone https://github.com/jason-weirather/IDP.git \
    && rm -r /Source/IDP/example \
    && pip install seq-tools==1.0.9
ENV PATH="/Source/IDP/bin:${PATH}"

## Include hisat2 as a more modern short read aligner
RUN cd /Source \
    && wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip \
    && unzip hisat2-2.1.0-Linux_x86_64.zip \
    && rm hisat2-2.1.0-Linux_x86_64.zip \
    && cd hisat2-2.1.0
ENV PATH="/Source/hisat2-2.1.0:${PATH}"

## Bring in samtools
RUN apt-get upgrade -y \
    && apt-get install -y \
    curl libncurses5-dev libbz2-dev liblzma-dev \
    && cd /Source \
    && curl -L https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 | tar -xj \
    && cd samtools-1.5 \
    && ./configure \
    && make \
    && make install \
    && cd /Source \
    && rm -r samtools-1.5