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Update bootstrap-fmriprep.sh #6

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Update bootstrap-fmriprep.sh #6

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18 changes: 9 additions & 9 deletions scripts/cubic/bootstrap-fmriprep.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -102,15 +102,15 @@ fi

## Add the containers as a subdataset
cd ${PROJECTROOT}
datalad clone ria+ssh://sciget.pmacs.upenn.edu:/project/bbl_projects/containers#~pennlinc-containers pennlinc-containers
# download the image so we don't ddos pmacs
cd pennlinc-containers
datalad get -r .
# get rid of the references to pmacs
set +e
datalad siblings remove -s pmacs-ria-storage
datalad siblings remove -s origin
set -e

# Clone the containers dataset. If specified on the command, use that path
CONTAINERDS=$2
if [[ ! -z "${CONTAINERDS}" ]]; then
datalad clone ${CONTAINERDS} pennlinc-containers
else
echo ERROR: requires a container dataset
exit 1
fi

cd ${PROJECTROOT}/analysis
datalad install -d . --source ${PROJECTROOT}/pennlinc-containers
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