troder/swiftortho repository overview

FROM continuumio/anaconda3
MAINTAINER Thomas Roder

RUN apt-get update --allow-releaseinfo-change && apt install -y \
  build-essential wget gcc g++ gfortran libopenblas-dev liblapack-dev pkg-config

# install MCL
WORKDIR /opt
RUN mkdir installmcl && \
  cd installmcl && \
  wget https://raw.githubusercontent.com/micans/mcl/main/install-this-mcl.sh -o install-this-mcl && \
  chmod u+x install-this-mcl.sh && \
  env HOME="/usr" bash -c ./install-this-mcl.sh && \
  cd /opt  && \
  rm -rf installmcl && \
  mcl --version  # test if it works

# cone SwiftOrtho
WORKDIR /opt
RUN git clone https://github.com/Rinoahu/SwiftOrtho.git

# install SwiftOrtho (remove last line)
WORKDIR /opt/SwiftOrtho
RUN bash install.sh
ENV PATH="/opt/SwiftOrtho/pypy/install_dir/bin/:${PATH}"
RUN pypy -mpip install -U networkx

WORKDIR /data

$ docker pull troder/swiftortho
$ docker run --rm -v $PWD:/data -it troder/swiftortho bash
(docker)$ pypy /opt/SwiftOrtho/bin/find_hit.py
(docker)$ pypy /opt/SwiftOrtho/bin/find_orth.py
(docker)$ pypy /opt/SwiftOrtho/bin/find_cluster.py
(docker)$ pypy /opt/SwiftOrtho/scripts/run_all.py