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phizaz/nofold

By phizaz

•Updated almost 9 years ago

Nofold 1.0.1 docker image

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phizaz/nofold repository overview

⁠Nofold 1.0.1 docker image

Original work from http://kim.bio.upenn.edu/software/nofold.shtml⁠

⁠What's in this Dockerfile

⁠Build

# build
docker build -t phizaz/nofold:1.0.1 .
# build with jupyter
docker build -t phizaz/nofold:1.0.1-jupyter -f Dockerfile.jupyter .

⁠Usage

# run
docker run -it --user=1000:1000 -v <src>:/home/docker/workdir phizaz/nofold:1.0.1 bash
# run with jupyter
docker run -it --rm --user=1000:1000 -v <src>:/home/docker/workdir -p 8888:8888 phizaz/nofold:1.0.1-jupyter --port=8888

Nofold source code is in /home/docker/nofold or ${NOFOLD}.

I suggest mount your working directory to /home/docker/workdir.

⁠Test

To test the usability of this Dockerfile after you have built the image, I have provided the copy-and-paste script here for your reproducibility.

The following snippet will perform these things:

  1. Get normalized structural coordinates of sequences:
  2. Extract any clusters that form within the structure space:
docker run -it --rm --user=1000:1000 \
    --workdir=/home/docker/nofold/src \
    phizaz/nofold:1.0.1 \
    bash -c "python score_and_normalize.py ../demo/demo1/demo1.db --cpus=4 \
        && python nofold_pipeline.py ../demo/demo1/demo1.zNorm.pcNorm100.zNorm.bitscore ../demo/demo1/demo1.db --cpus=4 --bounds-file=../thresh/bounds_30seq.txt --verbose \
        && bash"

Tag summary

Content type

Image

Digest

Size

507.9 MB

Last updated

almost 9 years ago

docker pull phizaz/nofold