This project aims at deploying a singularity container transparently, so that an application inside the container can be used without adjusting any scripts or pipelines (e.g. nipype). For building your own containers see examples in https://github.com/CAIsr/caid

Important: add bind points to .bashrc before executing this script

This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.:

export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data"

This gives you a list of available images:

curl -s -S -X GET https://swift.rc.nectar.org.au:8888/v1/AUTH_d6165cc7b52841659ce8644df1884d5e/singularityImages

clone repo into a folder with the intented image name

git clone https://github.com/CAIsr/transparent-singularity.git convert3d_1.0.0_20200420

install

this will create scripts for every binary in the container located in the $DEPLOY_PATH inside the container. It will also create activate and deactivate scripts and module files for lmod (https://lmod.readthedocs.io/en/latest/)

cd convert3d_1.0.0_20200420
./run_transparent_singularity.sh --container convert3d_1.0.0_20200420.sif

or when you want to install from the singularity registry (might be faster outside Australia):

cd convert3d_1.0.0_20200420
./run_transparent_singularity.sh --container convert3d_1.0.0_20200420.sif --storage sylabs

Use in module system LMOD

add the module folder path to $MODULEPATH

Manual acivation and deactivation (in case module system is not available). This will add the paths to the .bashrc

activate

source activate_minc_1p9p16_visual_20181022.simg.sh

deactivate

source deactivate_minc_1p9p16_visual_20181022.simg.sh

cleanup

./ts_cleanupCommands.sh

updating a container the quick and easy way:

list and pick name:

curl -s -S -X GET https://swift.rc.nectar.org.au:8888/v1/AUTH_d6165cc7b52841659ce8644df1884d5e/singularityImages

get:

curl -v -s -S -X GET https://swift.rc.nectar.org.au:8888/v1/AUTH_d6165cc7b52841659ce8644df1884d5e/singularityImages/insertCONTAINERname -O

likeajumprope/transparent-singularity