(unofficial) GraphProt - modeling binding preferences of RNA-binding proteins
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website: http://www.bioinf.uni-freiburg.de/Software/GraphProt/
Maticzka D, Lange SJ, Costa F, Backofen R. GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol. 2014;15(1):R17. Published 2014 Jan 22. doi:10.1186/gb-2014-15-1-r17
Part of plachta11b diploma. Compatible with rootless singularity using readonly filesystem.
In case of bugs or questions do not hesitate to write mail (short and simple)
FROM continuumio/miniconda:4.7.12 AS builder
RUN conda config --add channels bioconda \
&& conda config --add channels conda-forge
RUN conda create -n graphprot_env graphprot
# RUN conda create -n graphprot_env graphprot nomkl # slower version
RUN conda env list
RUN /bin/bash -c "source activate graphprot_env"
RUN conda list -e
# FROM python:3.6-slim AS conda
# COPY --from=builder /opt/conda/envs/graphprot_env /opt/conda/envs/graphprot_env
# ENV CONDA_PREFIX /opt/conda/envs/graphprot_env
# ENV PATH /opt/conda/envs/graphprot_env/bin:$PATH
# CMD [ "GraphProt.pl" ]
FROM continuumio/miniconda:4.7.12
RUN conda config --add channels bioconda \
&& conda config --add channels conda-forge
ADD ./requirements.txt /source/requirements.txt
RUN conda install --yes --freeze-installed --file /source/requirements.txt \
&& conda clean --all --force-pkgs-dirs --yes
SHELL ["conda", "run", "-n", "graphprot", "/bin/bash", "-c"]
ENV CONDA_PREFIX /opt/conda
CMD [ "GraphProt.pl" ]
# this dockerfile is just test to compare miniconda size against biocontainers image: docker pull quay.io/biocontainers/graphprot:1.1.7--h3445559_4
Content type
Image
Digest
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445.5 MB
Last updated
about 6 years ago
docker pull plachta11b/graphprot:0.1