PhyloCSF Dockerfile (basic)

Dockerfile

# Basic Dockerfile for PhyloCSF.
# Example usage:
#   docker build -t mlin:PhyloCSF https://gist.githubusercontent.com/mlin/31c0a7623f99d3bf3222/raw/Dockerfile
#   docker run -v /path/to/host/data:/data mlin:PhyloCSF 29mammals /data/input.fa
# PhyloCSF homepage: https://github.com/mlin/PhyloCSF/wiki
FROM ubuntu:trusty
MAINTAINER Mike Lin <[email protected]>
RUN apt-get update
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-suggests --no-install-recommends ca-certificates software-properties-common time git build-essential gfortran 
RUN add-apt-repository ppa:avsm/ppa
RUN apt-get update
RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-suggests --no-install-recommends -y ocaml camlp4 camlp4-extra opam libgsl0-dev m4 pkg-config
RUN opam init
RUN opam install -y batteries gsl ocaml+twt forkwork ounit should
RUN git clone --depth=1 git://github.com/mlin/PhyloCSF.git
WORKDIR /PhyloCSF
RUN eval $(opam config env) && make FORKWORK=1 && make -C src FORKWORK=1 testexe
ENV TIME \n    \t%E real,\t%U user,\t%S sys
RUN ["/bin/bash","-c","cd src && time ./test.native"]
ENTRYPOINT ["/PhyloCSF/PhyloCSF"]

I'm getting this error, anything I can do to fix?
The following packages have unmet dependencies: opam : Depends: opam-docs (= 1.1.1-1) but 1.2.2-1ppa2~trusty is to be installed E: Unable to correct problems, you have held broken packages. The command '/bin/sh -c DEBIAN_FRONTEND=noninteractive apt-get install --no-install-suggests --no-install-recommends -y ocaml camlp4 camlp4-extra opam libgsl0-dev m4 pkg-config' returned a non-zero code: 100

I'm getting the same error. Any fix for this issue?

I don't think there's a fix :( . I ended up getting phyloCSF from the bioconda channel. I think this may be the link I used: https://bioconda.github.io/recipes/phylocsf/README.html

Hope this helps!

I'm getting this error, anything I can do to fix?
The following packages have unmet dependencies: opam : Depends: opam-docs (= 1.1.1-1) but 1.2.2-1ppa2~trusty is to be installed E: Unable to correct problems, you have held broken packages. The command '/bin/sh -c DEBIAN_FRONTEND=noninteractive apt-get install --no-install-suggests --no-install-recommends -y ocaml camlp4 camlp4-extra opam libgsl0-dev m4 pkg-config' returned a non-zero code: 100

I'm getting the same error. Any fix for this issue?

I don't think there's a fix :( . I ended up getting phyloCSF from the bioconda channel. I think this may be the link I used: https://bioconda.github.io/recipes/phylocsf/README.html

Hope this helps!

Thank you!