Singularity
Neurodesk Singularity Containers
Our docker containers are converted to singularity containers and stored on Object storage.
Download Singularity Containers
First get an overview which containers are available as Singularity containers: https://github.com/NeuroDesk/neurodesk/blob/master/cvmfs/log.txt
curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/cvmfs/log.txt
assign the container name to a variable:
export container=itksnap_3.8.0_20201208
Then download the containers. An easy way is to use CURL (e.g. downloading from the US location):
curl -X GET https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg -O
or from australia
curl -X GET https://objectstorage.ap-sydney-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg -O
A faster way is pulling from multiple storage locations at once using aria2:
aria2c https://objectstorage.us-ashburn-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg https://objectstorage.eu-frankfurt-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg https://objectstorage.ap-sydney-1.oraclecloud.com/n/sd63xuke79z3/b/neurodesk/o/${container}.simg https://swift.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/${container}.simg
Transparent Singularity
The singularity containers can be also be used in combination with our Transparent Singularity Tool tool, that wraps the executables inside a container to make them easily available for pipelines. More information can be found here:
one example to do this is:
curl -s https://raw.githubusercontent.com/NeuroDesk/neurodesk/master/cvmfs/log.txt
export container=itksnap_3.8.0_20201208
git clone https://github.com/NeuroDesk/transparent-singularity ${container}
cd ${container}
./run_transparent_singularity.sh ${container}
Last modified
January 27, 2023
: Merge pull request #235 from iishiishii/issue-119 (4184046)