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The NCBI genome downloader is missing as a dependency. We installed via
Could this be added? |
gedankenstuecke
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gedankenstuecke
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I went through the whole file again and found some things that should be adapted before merging the image. :)
| # Base Image | ||
| FROM ncbihackathon/ncbihackathonbase:latest | ||
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| # Metadata |
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The meta data should be adapted to STREAMclean I think.
| cd / && \ | ||
| rm -rf $DST/$FOLDER | ||
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| # BAMTools 2.5.1 |
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We don't need BAMtools (if I'm not mistaken!)
| make install && \ | ||
| rm -rf $DST/$FOLDER $DST/$ZIP | ||
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| # STAR 2.5.3a |
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Star can be removed completely
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| USER biodocker | ||
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| RUN git clone --recursive https://github.com/NCBI-Hackathons/NanoporeMapper.git |
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The URL for the repo has changed to https://github.com/NCBI-Hackathons/STREAMclean.git (the old URL works as GitHub handles redirects when repos are renamed, but would probably be nicer to have a clean setup)
| mv $DST/$FOLDER/LICENSE $DST/$FOLDER/README /home/biodocker/bin/ && \ | ||
| mv $DST/$FOLDER/bin/* /home/biodocker/bin/ && \ | ||
| rm -rf $DST/$FOLDER | ||
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The python modules need to be installed in order for the pipeline to run. I guess
RUN cd ~/STREAMclean & pip install -r requirements.txt should do the trick?
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