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
This script expects that you have adjusted the Singularity Bindpoints in your .bashrc, e.g.:
export SINGULARITY_BINDPATH="/gpfs1/,/QRISdata,/data"
curl -s -S -X GET https://swift.rc.nectar.org.au:8888/v1/AUTH_d6165cc7b52841659ce8644df1884d5e/singularityImages
git clone https://github.com/CAIsr/transparent-singularity.git minc_1p9p16_visual_20181022
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 minc_1p9p16_visual_20181022
./run_transparent_singularity.sh minc_1p9p16_visual_20181022.simg
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
source activate_minc_1p9p16_visual_20181022.simg.sh
source deactivate_minc_1p9p16_visual_20181022.simg.sh
./ts_cleanupCommands.sh
rm activate_minc_1p9p16_visual_20181022.simg.sh
rm deactivate_minc_1p9p16_visual_20181022.simg.sh
rm commands.txt
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
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