containerized script for section1

@dbkeator @albertcrowley - perhaps you can test to see if this works.

mkdir section1
cd section1
docker run -i --rm kaczmarj/neurodocker:master generate singularity \
  --base neurodebian:latest --pkg-manager apt \
  --install graphviz git wget \
  --miniconda \
    conda_install="python=3 pytest graphviz pip reprozip reprounzip \
       requests rdflib fuzzywuzzy python-levenshtein pygithub pandas" \
    pip_install="owlready2 pybids duecredit \
     https://github.com/incf-nidash/PyNIDM/archive/a90b3f47dbdafb9504f13a3a8d85fdff931cc45c.zip" \
    create_env="section1" \
    activate=true \
  --run-bash "cd /opt && \
    git clone https://github.com/incf-nidash/PyNIDM.git" > Singularity

followed by:

sudo singularity build section1.img Singularity

for docker replace singularity/Singularity with docker/Dockerfile to generate the docker version. and then do: docker build -t section1:latest .

this pulls in the latest version. this is only being made available so people can create and do things outside the vm in containers. as far as i know the current plan is to install these tools in the main vm for the ohbm training.

Thanks. I tried that out in my copy of the NITRC-CE VM. It's not the final copy Matt is still working on so it doesn't have docker or singularity installed. Once I apt-get installed docker.io and singularity-container I was able to run through your steps. Inside the container I could then run my sample python scripts against BIDS datasets.

I'll pass this along to Jeff and Matt to see how they want to integrate it.

On Tue, Jun 5, 2018 at 9:36 AM Satrajit Ghosh notifications@github.com wrote:

@dbkeator https://github.com/dbkeator @albertcrowley https://github.com/albertcrowley - perhaps you can test to see if this works.

mkdir section1 cd section1 docker run -i --rm kaczmarj/neurodocker:master generate singularity \ --base neurodebian:latest --pkg-manager apt \ --install graphviz git wget \ --miniconda \ conda_install="python=3 pytest graphviz pip reprozip reprounzip \ requests rdflib fuzzywuzzy python-levenshtein pygithub pandas" \ pip_install="owlready2 pybids duecredit \ https://github.com/incf-nidash/PyNIDM/archive/a90b3f47dbdafb9504f13a3a8d85fdff931cc45c.zip" \ create_env="section1" \ activate=true \ --run-bash "cd /opt && \ git clone https://github.com/incf-nidash/PyNIDM.git" > Singularity

followed by:

sudo singularity build section1.img Singularity

for docker replace singularity/Singularity with docker/Dockerfile to generate the docker version. and then do: docker build -t section1:latest .

this pulls in the latest version. this is only being made available so people can create and do things outside the vm in containers. as far as i know the current plan is to install these tools in the main vm for the ohbm training.

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albertcrowley / nidm-training

containerized script for section1 #1