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Save mlin/31c0a7623f99d3bf3222 to your computer and use it in GitHub Desktop.
| # 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 <mlin@mlin.net> | |
| 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 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'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: 100I'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: 100I'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!
line 14 should be "ocaml-txt"