(unofficial) ssHMM - Sequence-Structure Hidden Markov Model
147
website: https://sshmm.readthedocs.io/en/latest/index.html
David Heller, Ralf Krestel, Uwe Ohler, Martin Vingron, Annalisa Marsico, ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data, Nucleic Acids Research, Volume 45, Issue 19, 2 November 2017, Pages 11004–11018, https://doi.org/10.1093/nar/gkx756
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 hellerd/sshmm:v1.0.5
# pip install --user nonroot_user should be used in base image
# hotfix TODO (create and change user instead)
RUN chmod -R 555 /usr/local/lib/python2.7/dist-packages/
RUN mkdir packages \
&& mv /root/RNAstructure /packages/RNAstructure \
&& mv /root/RNAshapes-2.1.6 /packages/RNAshapes-2.1.6
ENV PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/packages/RNAstructure/exe/:/packages/RNAshapes-2.1.6/src
ENV DATAPATH=/packages/RNAstructure/data_tables/
ADD ./preprocess.py /usr/local/bin/preprocess_fasta_dataset
RUN chmod +x /usr/local/bin/preprocess_fasta_dataset
RUN useradd -M guest
USER guest
CMD [ "train_seqstructhmm" ]
Content type
Image
Digest
Size
354.1 MB
Last updated
about 6 years ago
docker pull plachta11b/sshmm:0.1