diff --git a/.ci/check_py3_compatibility.sh b/.ci/check_py3_compatibility.sh
index 5b23a549cba..c61e1624453 100755
--- a/.ci/check_py3_compatibility.sh
+++ b/.ci/check_py3_compatibility.sh
@@ -7,15 +7,16 @@ else
 fi
 
 export ACK_OPTIONS=" --type python \
---ignore-dir=.git/ \
---ignore-dir=.tox/ \
---ignore-dir=.venv/ \
---ignore-dir=client/node_modules/ \
---ignore-dir=database/ \
---ignore-dir=doc/build/ \
---ignore-dir=eggs/ \
---ignore-dir=static/maps/ \
---ignore-dir=static/scripts/"
+--ignore-dir=.git \
+--ignore-dir=.tox \
+--ignore-dir=.venv \
+--ignore-dir=.venv3 \
+--ignore-dir=client/node_modules \
+--ignore-dir=database \
+--ignore-dir=doc/build \
+--ignore-dir=eggs \
+--ignore-dir=static/maps \
+--ignore-dir=static/scripts"
 
 PYTHON2_ONLY_MODULES="__builtin__ _winreg BaseHTTPServer CGIHTTPServer \
 ConfigParser Cookie cookielib copy_reg cPickle cStringIO Dialog dummy_thread \
diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt
index 6a17718a548..225a6f78b70 100644
--- a/.ci/flake8_blacklist.txt
+++ b/.ci/flake8_blacklist.txt
@@ -1,8 +1,12 @@
-.venv/
-.tox/
-client/node_modules/
-database/
+.git
+.tox
+.venv
+.venv3
+client/node_modules
+database
+doc/build
 doc/source/conf.py
-eggs/
+eggs
 lib/galaxy/util/jstree.py
-lib/galaxy/web/proxy/js/node_modules/
+static/maps
+static/scripts
diff --git a/.ci/flake8_wrapper.sh b/.ci/flake8_wrapper.sh
index 47395c0c32f..3330d52f35a 100755
--- a/.ci/flake8_wrapper.sh
+++ b/.ci/flake8_wrapper.sh
@@ -2,7 +2,7 @@
 
 set -e
 
-flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
+flake8 --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
 
 # Apply stricter rules for the directories shared with Pulsar
 flake8 --ignore=D --max-line-length=150 lib/galaxy/jobs/runners/util/
diff --git a/.ci/flake8_wrapper_docstrings.sh b/.ci/flake8_wrapper_docstrings.sh
index fa728303331..a8b9dd52bc2 100755
--- a/.ci/flake8_wrapper_docstrings.sh
+++ b/.ci/flake8_wrapper_docstrings.sh
@@ -15,7 +15,7 @@ args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
 
 if [ "$1" = "--include" ];
 then
-    flake8 $args `paste .ci/flake8_docstrings_include_list.txt`
+    flake8 $args $(paste -sd' ' .ci/flake8_docstrings_include_list.txt)
 else
-    flake8 $args --exclude `paste -sd, .ci/flake8_blacklist.txt` .
+    flake8 $args --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
 fi
diff --git a/.gitignore b/.gitignore
index b7f346d0953..3951ab3d741 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@ scripts/scramble/archives
 
 # Python virtualenv
 .venv
+.venv3
 
 # Database stuff
 database/beaker_sessions