diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index aae0334053b..29414b29d87 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -37,7 +37,7 @@ nodeenv = "*"
 pycryptodome = "*"
 uWSGI = "*"
 pysam = "==0.15.1"
-bdbag = "*"
+bdbag = "==1.4.1"  # 1.5.0 requires Python >=2.7.9
 bleach = "*"
 "bz2file" = {version = "*", markers = "python_version < '3.3'"}
 ipaddress = {version = "*", markers = "python_version < '3.3'"}
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index c33871500c5..4d68d12801c 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -5,7 +5,7 @@ argh==0.26.2
 atomicwrites==1.2.1
 attrs==18.2.0
 babel==2.6.0
-certifi==2018.10.15
+certifi==2018.11.29
 chardet==3.0.4
 commonmark==0.5.4
 docutils==0.14
@@ -15,28 +15,28 @@ idna==2.7
 imagesize==1.1.0
 jinja2==2.10
 lxml==4.2.5
-markupsafe==1.0
+markupsafe==1.1.0
 mock==2.0.0
 more-itertools==4.3.0
 nose==1.3.7
 nosehtml==0.4.5
-pathlib2==2.3.2 ; python_version < '3.6'
+pathlib2==2.3.3 ; python_version < '3.6'
 pathtools==0.1.2
-pbr==5.1.0
+pbr==5.1.1
 pluggy==0.8.0
 py==1.7.0
 pygithub3==0.5.1 ; python_version < '3'
-pygments==2.2.0
+pygments==2.3.0
 pytest-html==1.19.0
 pytest-metadata==1.7.0
 pytest-pythonpath==0.7.3
-pytest==3.9.2
-pytz==2018.6
+pytest==4.0.1
+pytz==2018.7
 pyyaml==3.13
 recommonmark==0.4.0
-requests==2.20.0
+requests==2.20.1
 scandir==1.9.0 ; python_version < '3.5'
-selenium==3.14.1
+selenium==3.141.0
 six==1.11.0
 snowballstemmer==1.2.1
 sphinx-rtd-theme==0.4.2
@@ -45,5 +45,5 @@ sphinxcontrib-websupport==1.1.0
 testfixtures==6.3.0
 twill==0.9.1 ; python_version < '3'
 typing==3.6.6 ; python_version < '3.5'
-urllib3==1.24
+urllib3==1.24.1
 watchdog==0.9.0
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index 737b810c102..b4ae3fc1e29 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -15,10 +15,10 @@ azure-mgmt-resource==2.0.0
 azure-mgmt-storage==2.0.0
 azure-nspkg==3.0.2
 azure-storage-blob==1.3.1
-azure-storage-common==1.3.0
-azure-storage-nspkg==3.0.0
+azure-storage-common==1.4.0
+azure-storage-nspkg==3.1.0
 babel==2.6.0
-bagit==1.7.0
+bagit==1.6.4
 bcrypt==3.1.4
 bdbag==1.4.1
 beaker==1.10.0
@@ -31,29 +31,29 @@ botocore==1.10.84
 bunch==1.0.1
 bx-python==0.8.2
 bz2file==0.98 ; python_version < '3.3'
-cachetools==2.1.0
-certifi==2018.10.15
+cachetools==3.0.0
+certifi==2018.11.29
 cffi==1.11.5
 chardet==3.0.4
 cheetah3==3.1.0
-cliff==2.13.0
+cliff==2.14.0
 cloudauthz==0.2.0
 cloudbridge==1.0.2
 cmd2==0.8.9
 contextlib2==0.5.5 ; python_version < '3.5'
-cryptography==2.3.1
+cryptography==2.4.2
 debtcollector==1.20.0
 decorator==4.3.0
 deprecation==2.0.6
 dictobj==0.4
 docopt==0.6.2
 docutils==0.14
-dogpile.cache==0.6.7
+dogpile.cache==0.6.8
 enum34==1.1.6 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version == '2.7'
-future==0.16.0
+future==0.17.1
 futures==3.2.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.3
 gxformat2==0.8.0
@@ -67,59 +67,59 @@ jmespath==0.9.3
 jsonpatch==1.23
 jsonpointer==2.0
 jsonschema==2.6.0
-keystoneauth1==3.11.0
+keystoneauth1==3.11.1
 kombu==4.2.1
 mako==1.0.7
-markupsafe==1.0
+markupsafe==1.1.0
 mercurial==3.7.3 ; python_version < '3'
 monotonic==1.5
-msgpack==0.5.6
+msgpack==0.6.0
 msrest==0.5.5
 msrestazure==0.5.0
 munch==2.3.2
 netaddr==0.7.19
 netifaces==0.10.7
 networkx==1.11
-nodeenv==1.3.2
+nodeenv==1.3.3
 nose==1.3.7
-numpy==1.15.3
+numpy==1.15.4
 oauthlib==2.1.0
 openstacksdk==0.17.0
 os-client-config==1.31.2
-os-service-types==1.3.0
+os-service-types==1.4.0
 osc-lib==1.11.1
-oslo.config==6.6.2
-oslo.context==2.21.0
-oslo.i18n==3.22.1
-oslo.log==3.40.1
+oslo.config==6.7.0
+oslo.context==2.22.0
+oslo.i18n==3.23.0
+oslo.log==3.42.0
 oslo.serialization==2.28.1
-oslo.utils==3.37.1
+oslo.utils==3.38.0
 packaging==18.0
 paramiko==2.4.2
 parsley==1.3
-paste==3.0.4
-pastedeploy==1.5.2
-pastescript==2.0.2
-pbr==5.1.0
+paste==3.0.5
+pastedeploy==2.0.1
+pastescript==3.0.0
+pbr==5.1.1
 prettytable==0.7.2
-psutil==5.4.7
+psutil==5.4.8
 pulsar-galaxy-lib==0.8.3
 pyasn1==0.4.4
 pycparser==2.19
-pycryptodome==3.6.6
-pycryptodomex==3.6.6
+pycryptodome==3.7.2
+pycryptodomex==3.7.2
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
-pyjwkest==1.4.0 ; extra == 'openidconnect'
-pyjwt==1.6.4
+pyjwkest==1.4.0
+pyjwt==1.7.0
 pykwalify==1.7.0
 pynacl==1.3.0
 pyopenssl==18.0.0
-pyparsing==2.2.2
+pyparsing==2.3.0
 pyperclip==1.7.0
 pysam==0.15.1
 pysftp==0.2.9
 python-cinderclient==4.0.0
-python-dateutil==2.7.3
+python-dateutil==2.7.5
 python-genomespaceclient==1.1.0
 python-glanceclient==2.12.0
 python-keystoneclient==3.17.0
@@ -127,37 +127,37 @@ python-neutronclient==6.9.0
 python-novaclient==11.0.0
 python-openid==2.2.5
 python-swiftclient==3.6.0
-pytz==2018.6
+pytz==2018.7
 pyyaml==3.13
 repoze.lru==0.7
 requests-oauthlib==1.0.0
 requests-toolbelt==0.8.0
-requests==2.20.0
+requests==2.20.1
 requestsexceptions==1.4.0
-rfc3986==1.1.0
+rfc3986==1.2.0
 routes==2.4.1
 s3transfer==0.1.13
 simplejson==3.16.0
 six==1.11.0
 social-auth-core[openidconnect]==1.5.0
 sqlalchemy-migrate==0.11.0
-sqlalchemy-utils==0.33.6
-sqlalchemy==1.2.12
+sqlalchemy-utils==0.33.9
+sqlalchemy==1.2.14
 sqlparse==0.2.4
 stevedore==1.30.0
 subprocess32==3.5.3 ; python_version < '3.0'
-svgwrite==1.1.12
+svgwrite==1.2.1
 tempita==0.5.2
 tenacity==4.12.0
 typing==3.6.6 ; python_version < '3.5'
 tzlocal==1.5.1
 unicodecsv==0.14.1 ; python_version < '3.0'
-urllib3==1.24
+urllib3==1.24.1
 uwsgi==2.0.17.1
 vine==1.1.4
 warlock==1.3.0
 wcwidth==0.1.7 ; sys_platform != 'win32'
 webencodings==0.5.1
-webob==1.8.3
+webob==1.8.4
 whoosh==2.7.4
 wrapt==1.10.11
diff --git a/lib/galaxy/dependencies/pipfiles/update.sh b/lib/galaxy/dependencies/pipfiles/update.sh
index 5dbe6ca7b22..711e0595388 100755
--- a/lib/galaxy/dependencies/pipfiles/update.sh
+++ b/lib/galaxy/dependencies/pipfiles/update.sh
@@ -42,7 +42,8 @@ for env in $ENVS; do
     pipenv lock -r | sed -e 's/--hash[^[:space:]]*//g' -e 's/[[:space:]]*$//' > pinned-requirements.txt
     pipenv lock -r --dev | sed -e 's/--hash[^[:space:]]*//g' -e 's/[[:space:]]*$//' > pinned-dev-requirements.txt
     # Fix oscillating environment markers
-    sed -i.orig -e "s/^cffi==\([^ ;]\{1,\}\).*$/cffi==\1/" \
+    sed -i.orig -e "s/^azure-storage-nspkg==\([^ ;]\{1,\}\).*$/azure-storage-nspkg==\1/" \
+                -e "s/^cffi==\([^ ;]\{1,\}\).*$/cffi==\1/" \
                 -e "s/^cmd2==\([^ ;]\{1,\}\).*$/cmd2==\1/" \
                 -e "s/^enum34==\([^ ;]\{1,\}\).*$/enum34==\1 ; python_version < '3.4'/" \
                 -e "s/^funcsigs==\([^ ;]\{1,\}\).*$/funcsigs==\1 ; python_version < '3.3'/" \