diff --git a/delete_userless_histories.sh b/delete_userless_histories.sh
deleted file mode 100644
index 7673537daca..00000000000
--- a/delete_userless_histories.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 10 -2 $@ >> ./delete_userless_histories.log
diff --git a/delete_userless_histories_main.sh b/delete_userless_histories_main.sh
deleted file mode 100644
index fe1600ef54f..00000000000
--- a/delete_userless_histories_main.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 $@ >> ./delete_userless_histories.log
diff --git a/purge_datasets.sh b/purge_datasets.sh
deleted file mode 100644
index dd5d6739e1f..00000000000
--- a/purge_datasets.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 10 -6 -r $@ >> ./purge_datasets.log
diff --git a/purge_datasets_main.sh b/purge_datasets_main.sh
deleted file mode 100644
index 0bd49f9a746..00000000000
--- a/purge_datasets_main.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./purge_datasets.log
diff --git a/purge_histories.sh b/purge_histories.sh
deleted file mode 100644
index e18cdca8d37..00000000000
--- a/purge_histories.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./purge_histories.log
diff --git a/purge_histories_main.sh b/purge_histories_main.sh
deleted file mode 100644
index 343b1675b65..00000000000
--- a/purge_histories_main.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./purge_histories.log
diff --git a/scripts/cleanup_datasets.py b/scripts/cleanup_datasets/cleanup_datasets.py
similarity index 100%
rename from scripts/cleanup_datasets.py
rename to scripts/cleanup_datasets/cleanup_datasets.py
diff --git a/scripts/cleanup_datasets/delete_userless_histories.sh b/scripts/cleanup_datasets/delete_userless_histories.sh
new file mode 100644
index 00000000000..cd16f528b41
--- /dev/null
+++ b/scripts/cleanup_datasets/delete_userless_histories.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/purge_delete_userless_histories.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -2 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log
diff --git a/scripts/cleanup_datasets/delete_userless_histories_main.sh b/scripts/cleanup_datasets/delete_userless_histories_main.sh
new file mode 100644
index 00000000000..e0c486336a0
--- /dev/null
+++ b/scripts/cleanup_datasets/delete_userless_histories_main.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/delete_userless_histories_main.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 $@ >> ./scripts/cleanup_datasets/delete_userless_histories_main.log
diff --git a/scripts/cleanup_datasets/purge_datasets.sh b/scripts/cleanup_datasets/purge_datasets.sh
new file mode 100644
index 00000000000..edd0ec005dd
--- /dev/null
+++ b/scripts/cleanup_datasets/purge_datasets.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/purge_datasets.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log
diff --git a/scripts/cleanup_datasets/purge_datasets_main.sh b/scripts/cleanup_datasets/purge_datasets_main.sh
new file mode 100644
index 00000000000..64737d2eb1f
--- /dev/null
+++ b/scripts/cleanup_datasets/purge_datasets_main.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/purge_datasets_main.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./scripts/cleanup_datasets/purge_datasets_main.log
diff --git a/scripts/cleanup_datasets/purge_histories.sh b/scripts/cleanup_datasets/purge_histories.sh
new file mode 100644
index 00000000000..438aef72574
--- /dev/null
+++ b/scripts/cleanup_datasets/purge_histories.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/purge_histories.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log
diff --git a/scripts/cleanup_datasets/purge_histories_main.sh b/scripts/cleanup_datasets/purge_histories_main.sh
new file mode 100644
index 00000000000..f693ad43196
--- /dev/null
+++ b/scripts/cleanup_datasets/purge_histories_main.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/purge_histories_main.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./scripts/cleanup_datasets/purge_histories_main.log
diff --git a/scripts/remove_renamed_datasets_from_disk.py b/scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
similarity index 100%
rename from scripts/remove_renamed_datasets_from_disk.py
rename to scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
diff --git a/scripts/rename_purged_datasets.py b/scripts/cleanup_datasets/rename_purged_datasets.py
similarity index 100%
rename from scripts/rename_purged_datasets.py
rename to scripts/cleanup_datasets/rename_purged_datasets.py
diff --git a/scripts/update_dataset_size.py b/scripts/cleanup_datasets/update_dataset_size.py
similarity index 100%
rename from scripts/update_dataset_size.py
rename to scripts/cleanup_datasets/update_dataset_size.py
diff --git a/scripts/update_metadata.py b/scripts/cleanup_datasets/update_metadata.py
similarity index 100%
rename from scripts/update_metadata.py
rename to scripts/cleanup_datasets/update_metadata.py
diff --git a/scripts/cleanup_datasets/update_metadata.sh b/scripts/cleanup_datasets/update_metadata.sh
new file mode 100644
index 00000000000..f9d036c0cc9
--- /dev/null
+++ b/scripts/cleanup_datasets/update_metadata.sh
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# This script must be executed from the $UNIVERSE_HOME directory
+# e.g., sh ./scripts/cleanup_datasets/update_metadata.sh
+
+. ./scripts/get_python.sh
+. ./setup_paths.sh
+
+$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./universe_wsgi.ini $@
diff --git a/update_metadata.sh b/update_metadata.sh
deleted file mode 100644
index 5f449763c48..00000000000
--- a/update_metadata.sh
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/sh
-
-. ./scripts/get_python.sh
-. ./setup_paths.sh
-
-$GALAXY_PYTHON ./scripts/update_metadata.py universe_wsgi.ini $@