Commit 31792e92 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz

Updated dockerfile

parent ddf670d0
FROM ubuntu:14.04
FROM conda/miniconda3
MAINTAINER Jindrich Vimr <jvimr@softeu.com>
RUN apt-get update && apt-get install -y git wget
RUN echo "1.565.1" > .lts-version-number
RUN conda create --name bigscape
#RUN source activate bigscape
RUN [ "/bin/bash", "-c","source activate bigscape"]
RUN conda install -y \
numpy \
scipy \
scikit-learn
RUN apt-get update && apt-get install -y wget curl git
RUN curl -LO http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
RUN bash Miniconda-latest-Linux-x86_64.sh -p /miniconda -b
RUN rm Miniconda-latest-Linux-x86_64.sh
ENV PATH=/miniconda/bin:${PATH}
RUN conda update -y conda
RUN conda install -y \
numpy \
scipy \
cython
RUN conda install -c bioconda hmmer biopython
#RUN pip install pysapc
RUN apt-get -y install build-essential \
&& rm -rf /var/lib/apt/lists/* \
&& pip install pysapc \
&& apt-get purge -y --auto-remove build-essential
RUN conda install -c bioconda hmmer biopython fasttree
RUN conda install -c anaconda networkx
WORKDIR /usr/src
## Cloning BiG-SCAPE
RUN git clone https://git.wur.nl/medema-group/BiG-SCAPE.git
## geting pFAMi
## geting Pfam
RUN wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/Pfam-A.hmm.gz
#ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz.
RUN gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm && mv Pfam-A.* /usr/src/BiG-SCAPE/.
#RUN mv BiG-SCAPE /opt/BiG-SCAPE
ENV PATH=/usr/src/BiG-SCAPE:${PATH}
RUN chmod +x /usr/src/BiG-SCAPE/*py
RUN chmod 777 /home
ENV PATH /usr/src/BiG-SCAPE:$PATH
USER 1000:1000
RUN mkdir /home/input /home/output
WORKDIR /home
ENTRYPOINT ["bigscape.py"]
CMD ["--help"]
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