From 16de087d093bcc56850066c26fbf20e4e79c0cad Mon Sep 17 00:00:00 2001
From: Tinashe Michael Tapera <tinashemtapera@gmail.com>
Date: Tue, 10 Aug 2021 14:03:48 -0400
Subject: [PATCH] Update bootstrap-fmriprep.sh

---
 scripts/cubic/bootstrap-fmriprep.sh | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/scripts/cubic/bootstrap-fmriprep.sh b/scripts/cubic/bootstrap-fmriprep.sh
index 1c00bae..55f2d88 100644
--- a/scripts/cubic/bootstrap-fmriprep.sh
+++ b/scripts/cubic/bootstrap-fmriprep.sh
@@ -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