...
Available as Apptainer and aliasing enabled, both apptainer --version
and singularity --version
will work. There are NeSI/Mahuika based notes on building containers HERE
Example
Code Block |
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# QIIME1
module purge
module load Apptainer/1.2.5
# recent Apptainer modules set APPTAINER_BIND, which typically breaks
# container builds, so unset it here
unset APPTAINER_BIND
# create a build and cache directory on scratch storage
export APPTAINER_CACHEDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_cache"
export APPTAINER_TMPDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_tmpdir"
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
setfacl -b $APPTAINER_TMPDIR
# pull the container
apptainer pull docker://mgrast/qiime:1.0
# execute the container
apptainer exec qiime_1.0.sif align_seqs.py -h |