Public | Automated Build

Last pushed: 13 days ago
Short Description
Docker build for repronim simple workflow
Full Description

Integration Testing:

Note: This demo is intended to run on OS X and GNU/Linux environments, but you can use the Docker container to run on any system you can run Docker or Singularity on.

Notice for commercial use

The following non-free Debian packages are part of the Docker container:

non-free/science fsl-5.0-core
non-free/science fsl-atlases, fsl-first-data

If you are considering commercial use of the container please consult the relevant license.

Information queried from NITRC-IR and stored in a google spreadsheet

https://docs.google.com/spreadsheets/d/11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA

1. To execute demo with Docker

First download the image

docker pull repronim/simple_workflow:latest

Now you can run the image as follows to test on 1 participant's data:

docker run -it --rm -v $PWD/output:/opt/repronim/simple_workflow/scripts/output \
   repronim/simple_workflow:latest run_demo_workflow.py \
   --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA -n 1 
docker run -it --rm -v $PWD/output:/opt/repronim/simple_workflow/scripts/output \
   repronim/simple_workflow:latest check_output.py --ignoremissing

You can extend this to all participants as follows.

docker run -it --rm -v $PWD/output:/opt/repronim/simple_workflow/scripts/output \
   repronim/simple_workflow:latest run_demo_workflow.py \
   --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA
docker run -it --rm -v $PWD/output:/opt/repronim/simple_workflow/scripts/output \
   repronim/simple_workflow:latest check_output.py

2. To execute demo within your current environment

The script will check for availability of the following:

  1. FSL
  2. curl
  3. git or unzip

Download the script

curl -Ok https://raw.githubusercontent.com/ReproNim/simple_workflow/3a64f3ffdf174e7c8970de620aa62a9167e3134f/Simple_Prep.sh

Setup the environment.

This will setup a complete environment within a directory
called simple_workflow. It will not add anything to your existing environment.

Note: Because of some limitations with the underlying packages, it may determine
that your current working directory path is too long and will ask you to move to
a shorter directory path.

bash Simple_Prep.sh

Execute a single subject test.

bash Simple_Prep.sh test

Run the full demo on all subjects

Option 1:

bash Simple_Prep.sh replay

Option 2: To use the newly created environment

cd simple_workflow/scripts
export OLDPATH=$PATH
export PATH=$PWD/../miniconda/envs/bh_demo/bin:$PATH

Now you can run the demo script

python run_demo_workflow.py --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA
python check_output.py

To run on one subject you can do:

python run_demo_workflow.py --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA -n 1

To restore old environment do:

export PATH=$OLDPATH
unset OLDPATH

3. To build docker image with custom environment

Using containerization solutions, such as Docker, allows to create
multiple complete computation environments while varying versions of any
analysis pipeline components or inputs. You could use Simple_Prep_docker
script to generate environments based on previous Debian or Ubuntu releases
for which NeuroDebian builds of FSL were available in the past.

N.B. ATM NeuroDebian snapshots repository is not widely open yet, so if
you would like to browse it, please "knock" first by running
curl -s http://neuro.debian.net/_files/knock-snapshots command in your shell.

Generate an environment

For the current test data, we generated an environment based on Debian jessie
release with FSL 5.0.9 that was available in April 2017:

/Simple_Prep_docker jessie 20170410T000000Z

which will generate a local docker image repronim:simple_prep_${USER}_jessie_20170410T000000Z
(${USER} will correspond to your user name), with all necessary for computation
components installed.

You can then run the demo using the docker image run commands above by replacing
repronim/simple_workflow:latest with repronim:simple_prep_${USER}_jessie_20170410T000000Z

Changing the FSL version

You can also generate an environment based on Debian jessie
release with FSL 5.0.8-3 as it was available in March of 2015 by
simply changing the timestamp:

./Simple_Prep_docker jessie 20150306T060524Z

which will generate a local docker image repronim:simple_prep_${USER}_jessie_20150306T060524Z
(${USER} will correspond to your user name), with all necessary for computation
components installed.

You can then run the demo using the docker image run commands above by replacing
repronim/simple_workflow:latest with repronim:simple_prep_${USER}_jessie_20150306T060524Z

4. Other containers

You can also use Singularity to run the docker
image from DockerHub. The following commands require the development branch (post release 2.2)
or release 2.3.

singularity create -s 4000 repronim.img
singularity import repronim.img docker://repronim/simple_workflow:latest
singularity run -B $PWD/output:/opt/repronim/simple_workflow/scripts/output -c \
  --pwd /opt/repronim/simple_workflow/scripts/ repronim.img run_demo_workflow.py \
  --key 11an55u9t2TAf0EV2pHN0vOd8Ww2Gie-tHp9xGULh_dA -n 1
singularity run -B $PWD/output:/opt/repronim/simple_workflow/scripts/output -c \
  --pwd /opt/repronim/simple_workflow/scripts/ repronim.img check_output.py --ignoremissing
Docker Pull Command
Owner
repronim
Source Repository

Comments (0)