fgajardoe/meme repository overview

# create a folder for the whole meme-chip run and include input fasta
mkdir run
cp input.fasta run/.

# run meme-chip
docker run -v /absolute/path/to/run/:/home/biodev/ fgajardoe/meme:lastest meme-chip -oc . -time 300 -ccut 100 -order 1 -db /db/EUKARYOTE/jolma2013.meme -db /db/JASPAR/JASPAR2018_CORE_vertebrates_non-redundant.meme -db /db/MOUSE/uniprobe_mouse.meme -meme-mod zoops -meme-minw 6 -meme-maxw 30 -meme-nmotifs 3 -meme-searchsize 100000 -dreme-e 0.05 -centrimo-score 5.0 -centrimo-ethresh 10.0 input.fasta

FROM debian:testing
LABEL maintainer Felipe Gajardo <[email protected]>
# Modified from Diego Diez's image (ddiez/meme:lastest)

# Add \_X wih X being the patch number (if needed).
ENV VERSION=5.1.1

# Install software.
RUN apt-get update && \
    apt-get install -y \
      build-essential \
      python \
      python3 \
      zlib1g-dev \
      libopenmpi-dev openmpi-bin \
      ssh \
      libxml2 \
      libxslt1.1 \
      libxml2-dev \
      libxslt1-dev \
      ghostscript \
      libxml-sax-expat-perl \
      curl \
      && \
    cpan install XML::Simple HTML::Treebuilder JSON && \
    curl http://meme-suite.org/meme-software/$VERSION/meme-$VERSION.tar.gz > /tmp/meme-$VERSION.tar.gz && \
    cd /tmp && tar xfzv meme-$VERSION.tar.gz && \
    cd /tmp/meme-$VERSION && \
    ./configure --prefix /opt && \
    make && \
    make install && \
    rm /tmp/meme-$VERSION.tar.gz && \
    rm -rf /tmp/meme-$VERSION && \
    cd /tmp && \
    curl http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.19.tgz > /tmp/motif_databases.12.19.tgz && \
    tar xf /tmp/motif_databases.12.19.tgz && \
    rm /tmp/motif_databases.12.19.tgz && \
    mv /tmp/motif_databases /db && \
    apt-get purge -y \
      build-essential \
      zlib1g-dev \
      libopenmpi-dev \
      libxml2-dev \
      libxslt1-dev \
      curl \
      && \
    apt-get autoremove -y

# Add /opt/bin to PATH.
ENV PATH /opt/bin:$PATH

# Set user.
RUN useradd -ms /bin/bash biodev
RUN echo 'biodev:biodev' | chpasswd
USER biodev
WORKDIR /home/biodev

CMD ["/bin/bash"]