(unofficial) MDS^2 - Motif Discovery on Short nucleotide Sequences
97
website: http://cse-jcui-08.unl.edu:7000/input
Please cite the following paper if you use MDS2: Gao T, Shu J, Cui J. A systematic approach to RNA-associated motif discovery. BMC Genomics. 2018 Feb 14;19(1). 146.
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 install --yes --freeze-installed scipy joblib python-igraph numpy bitarray weblogo python-graphviz
RUN mkdir /source && conda list -e | tee /source/requirements.txt
FROM continuumio/miniconda:4.7.12
#COPY --from=builder /source /source
ADD ./MDS2.tar.gz /source
ADD ./requirements.txt /source
RUN conda config --add channels bioconda \
&& conda config --add channels conda-forge
RUN conda install --yes --freeze-installed --file /source/requirements.txt \
&& conda clean --all --force-pkgs-dirs --yes
WORKDIR /source/MDS2
RUN sed -i "s#args=('log.txt','w')#args=('/output/mds_2_log.txt','w')#" /source/MDS2/loggingConf.ini
CMD ["python", "/source/MDS2/GraphBasedMotifFinding.py"]
Content type
Image
Digest
Size
276.6 MB
Last updated
about 6 years ago
docker pull plachta11b/mds2:0.1