From b0a7e651a622f22fe05977911c08efa8cf3b0b3e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:46:52 -0400
Subject: [PATCH 01/50] Prep 20.05 release of galaxy-objectstore.

---
 packages/objectstore/HISTORY.rst                          | 4 ++--
 packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index 52c2df7066e..3f0cf3174b5 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -6,10 +6,10 @@ History
 .. to_doc
 
 ---------------------
-19.9.1.dev0
+20.5.0.dev0
 ---------------------
 
-
+* First release from the 20.05 branch of Galaxy.
 
 ---------------------
 19.9.0 (2019-12-16)
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index 8389a7251b6..ad72d6781c5 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From e2460bdf5931323adfe6da84baf6588c612254f8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:47:17 -0400
Subject: [PATCH 02/50] Version 20.5.0 of objectstore (tag
 galaxy-objectstore-20.5.0).

---
 packages/objectstore/HISTORY.rst                          | 2 +-
 packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index 3f0cf3174b5..2b1b2ac05d8 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index ad72d6781c5..d2435ecdf12 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 16f0aff19064da5f63de198676396cb2ceae8944 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:47:37 -0400
Subject: [PATCH 03/50] Starting work on objectstore 20.5.1

---
 packages/objectstore/HISTORY.rst                          | 6 ++++++
 packages/objectstore/galaxy/project_galaxy_objectstore.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst
index 2b1b2ac05d8..7879816905a 100644
--- a/packages/objectstore/HISTORY.rst
+++ b/packages/objectstore/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index d2435ecdf12..cc83b9e9564 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From aad5865ec8e248d77b63904747103fe7b7805945 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:50:05 -0400
Subject: [PATCH 04/50] Prep 20.05 release of galaxy-job-metrics

---
 packages/job_metrics/HISTORY.rst                          | 4 ++--
 packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
index 52c2df7066e..3f0cf3174b5 100644
--- a/packages/job_metrics/HISTORY.rst
+++ b/packages/job_metrics/HISTORY.rst
@@ -6,10 +6,10 @@ History
 .. to_doc
 
 ---------------------
-19.9.1.dev0
+20.5.0.dev0
 ---------------------
 
-
+* First release from the 20.05 branch of Galaxy.
 
 ---------------------
 19.9.0 (2019-12-16)
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
index 1a710fcca5a..096aae4c567 100644
--- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-job-metrics"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From e03d2d71b36753c71d81d4fd6c07d01801846517 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:50:25 -0400
Subject: [PATCH 05/50] Version 20.5.0 of job-metrics (tag
 galaxy-job-metrics-20.5.0).

---
 packages/job_metrics/HISTORY.rst                          | 2 +-
 packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
index 3f0cf3174b5..2b1b2ac05d8 100644
--- a/packages/job_metrics/HISTORY.rst
+++ b/packages/job_metrics/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
index 096aae4c567..f7fb2ee0b4b 100644
--- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-job-metrics"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 649bb2f5c8496c5346f2f183ab53f59b95a2b4c5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:50:45 -0400
Subject: [PATCH 06/50] Starting work on job-metrics 20.5.1

---
 packages/job_metrics/HISTORY.rst                          | 6 ++++++
 packages/job_metrics/galaxy/project_galaxy_job_metrics.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst
index 2b1b2ac05d8..7879816905a 100644
--- a/packages/job_metrics/HISTORY.rst
+++ b/packages/job_metrics/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
index f7fb2ee0b4b..1b7831b5354 100644
--- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-job-metrics"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From d8f5b9219918602b667fac179462300bb2cbcea6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 09:59:57 -0400
Subject: [PATCH 07/50] Prep 20.05 release of galaxy-containers.

---
 packages/containers/HISTORY.rst                         | 4 ++--
 packages/containers/galaxy/project_galaxy_containers.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/containers/HISTORY.rst b/packages/containers/HISTORY.rst
index 52c2df7066e..3f0cf3174b5 100644
--- a/packages/containers/HISTORY.rst
+++ b/packages/containers/HISTORY.rst
@@ -6,10 +6,10 @@ History
 .. to_doc
 
 ---------------------
-19.9.1.dev0
+20.5.0.dev0
 ---------------------
 
-
+* First release from the 20.05 branch of Galaxy.
 
 ---------------------
 19.9.0 (2019-12-16)
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
index 54af538bb38..20e84f91e44 100644
--- a/packages/containers/galaxy/project_galaxy_containers.py
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.1.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-containers"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 601d1716cd66cd57faf75a408702711d336357b4 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:00:22 -0400
Subject: [PATCH 08/50] Version 20.5.0 of containers (tag
 galaxy-containers-20.5.0).

---
 packages/containers/HISTORY.rst                         | 2 +-
 packages/containers/galaxy/project_galaxy_containers.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/containers/HISTORY.rst b/packages/containers/HISTORY.rst
index 3f0cf3174b5..2b1b2ac05d8 100644
--- a/packages/containers/HISTORY.rst
+++ b/packages/containers/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
index 20e84f91e44..580245fd875 100644
--- a/packages/containers/galaxy/project_galaxy_containers.py
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-containers"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 6b5b64f04e1d37fadd16c2ca492951270fcdc78f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:00:43 -0400
Subject: [PATCH 09/50] Starting work on containers 20.5.1

---
 packages/containers/HISTORY.rst                         | 6 ++++++
 packages/containers/galaxy/project_galaxy_containers.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/containers/HISTORY.rst b/packages/containers/HISTORY.rst
index 2b1b2ac05d8..7879816905a 100644
--- a/packages/containers/HISTORY.rst
+++ b/packages/containers/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
index 580245fd875..8d1702ac5a9 100644
--- a/packages/containers/galaxy/project_galaxy_containers.py
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-containers"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From b1711d4fea5f088f8952b28bd6bbbfe1a08e5bad Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:01:54 -0400
Subject: [PATCH 10/50] Version 20.5.0 of tool-util (tag
 galaxy-tool-util-20.5.0).

---
 packages/tool_util/HISTORY.rst                        | 4 ++--
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index d2be3810139..3ecef776533 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -6,13 +6,13 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
 
 ---------------------
-20.1.0.dev0
+20.1.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.01 branch of Galaxy.
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index e1595d959a7..6e2e206f7f4 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev3'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 1d78f9120d05ad4fdc633dc164121ef38c9d243d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:02:12 -0400
Subject: [PATCH 11/50] Starting work on tool-util 20.5.1

---
 packages/tool_util/HISTORY.rst                        | 6 ++++++
 packages/tool_util/galaxy/project_galaxy_tool_util.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst
index 3ecef776533..6524c304020 100644
--- a/packages/tool_util/HISTORY.rst
+++ b/packages/tool_util/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index 6e2e206f7f4..42a4eb677a4 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From c74fd4925ddbd905000655995e11a883a3f85913 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:04:21 -0400
Subject: [PATCH 12/50] Prep release of galaxy-data version 20.05.

---
 packages/data/HISTORY.rst                   | 5 +++--
 packages/data/galaxy/project_galaxy_data.py | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index ec2f0e746e9..e82b1ccfc1d 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -5,8 +5,9 @@ History
 
 .. to_doc
 
+
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index 1a2efe784b6..6659659a547 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev1'
+__version__ = '20.5.0.dev1'
 
 PROJECT_NAME = "galaxy-data"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 4c802d19c0f981555cbc0bc9c2490a1eacdd42da Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:04:45 -0400
Subject: [PATCH 13/50] Version 20.5.0 of data (tag galaxy-data-20.5.0).

---
 packages/data/HISTORY.rst                   | 2 +-
 packages/data/galaxy/project_galaxy_data.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index e82b1ccfc1d..b7241d4b700 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -7,7 +7,7 @@ History
 
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index 6659659a547..1f171ea031c 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev1'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-data"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From bfdcc8bd129f5e2d266915975ae8de8be79e1677 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:05:21 -0400
Subject: [PATCH 14/50] Starting work on data 20.5.1

---
 packages/data/HISTORY.rst                   | 6 ++++++
 packages/data/galaxy/project_galaxy_data.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst
index b7241d4b700..4f7ba0c7b9d 100644
--- a/packages/data/HISTORY.rst
+++ b/packages/data/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 
 ---------------------
 20.5.0 (2020-07-04)
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index 1f171ea031c..25e11b314df 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-data"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 199d082dc231cdbd870c4d6e4b367393ceddc1d6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:07:43 -0400
Subject: [PATCH 15/50] Prep the 20.5 release of galaxy-job-execution.

---
 packages/job_execution/HISTORY.rst                            | 4 ++--
 packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/job_execution/HISTORY.rst
+++ b/packages/job_execution/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
index f2c11c58e0e..ba8e0888669 100644
--- a/packages/job_execution/galaxy/project_galaxy_job_execution.py
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-job-execution"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 58f4a5e7c0ef40ce5faf7b21f241d5bafe487de3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:08:48 -0400
Subject: [PATCH 16/50] Version 20.5.0 of job-execution (tag
 galaxy-job-execution-20.5.0).

---
 packages/job_execution/HISTORY.rst                            | 2 +-
 packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/job_execution/HISTORY.rst
+++ b/packages/job_execution/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
index ba8e0888669..2a918a40c77 100644
--- a/packages/job_execution/galaxy/project_galaxy_job_execution.py
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-job-execution"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From d678d55c11eccac9355c60c4006ee757cf511a5c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:09:04 -0400
Subject: [PATCH 17/50] Starting work on job-execution 20.5.1

---
 packages/job_execution/HISTORY.rst                          | 6 ++++++
 .../job_execution/galaxy/project_galaxy_job_execution.py    | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/job_execution/HISTORY.rst
+++ b/packages/job_execution/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
index 2a918a40c77..c88e1f230ac 100644
--- a/packages/job_execution/galaxy/project_galaxy_job_execution.py
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-job-execution"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 0611463b8e604da00781c97fccc58f6f1895014f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:10:11 -0400
Subject: [PATCH 18/50] Prep release of galaxy-auth 20.5.

---
 packages/auth/HISTORY.rst                   | 4 ++--
 packages/auth/galaxy/project_galaxy_auth.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/auth/HISTORY.rst
+++ b/packages/auth/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
index dbd94f1ced5..c39c2cd20c7 100644
--- a/packages/auth/galaxy/project_galaxy_auth.py
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-auth"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 3ec7ad24fe6b821d157404caa497cc3ede2ac48b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:10:28 -0400
Subject: [PATCH 19/50] Version 20.5.0 of auth (tag galaxy-auth-20.5.0).

---
 packages/auth/HISTORY.rst                   | 2 +-
 packages/auth/galaxy/project_galaxy_auth.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/auth/HISTORY.rst
+++ b/packages/auth/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
index c39c2cd20c7..006998b784b 100644
--- a/packages/auth/galaxy/project_galaxy_auth.py
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-auth"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From aa941c869b6eda97f57fbeb7e6522a84888a71ad Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:10:45 -0400
Subject: [PATCH 20/50] Starting work on auth 20.5.1

---
 packages/auth/HISTORY.rst                   | 6 ++++++
 packages/auth/galaxy/project_galaxy_auth.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/auth/HISTORY.rst
+++ b/packages/auth/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
index 006998b784b..a15658b18cb 100644
--- a/packages/auth/galaxy/project_galaxy_auth.py
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-auth"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 5302b58248c8c5a1b1fa211adf88e98c38cdd928 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:12:56 -0400
Subject: [PATCH 21/50] Prep release of galaxy-web-stack-20.5.0

---
 packages/web_stack/HISTORY.rst                        | 4 ++--
 packages/web_stack/galaxy/project_galaxy_web_stack.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/web_stack/HISTORY.rst
+++ b/packages/web_stack/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py
index 987fdbbd1fd..628611f8484 100644
--- a/packages/web_stack/galaxy/project_galaxy_web_stack.py
+++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-web-stack"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 89d001abb77ee6b92904760d5cf896a95eb124c9 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:13:09 -0400
Subject: [PATCH 22/50] Version 20.5.0 of web-stack (tag
 galaxy-web-stack-20.5.0).

---
 packages/web_stack/HISTORY.rst                        | 2 +-
 packages/web_stack/galaxy/project_galaxy_web_stack.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/web_stack/HISTORY.rst
+++ b/packages/web_stack/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py
index 628611f8484..5e6ca3835ac 100644
--- a/packages/web_stack/galaxy/project_galaxy_web_stack.py
+++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-web-stack"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 48e1e26acb7c9e53b38f00c4579fc02ba9e904ab Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:13:29 -0400
Subject: [PATCH 23/50] Starting work on web-stack 20.5.1

---
 packages/web_stack/HISTORY.rst                        | 6 ++++++
 packages/web_stack/galaxy/project_galaxy_web_stack.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/web_stack/HISTORY.rst
+++ b/packages/web_stack/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py
index 5e6ca3835ac..a454a258c8d 100644
--- a/packages/web_stack/galaxy/project_galaxy_web_stack.py
+++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-web-stack"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 78273d298880d2ebc0c526ab03a36e63c152af8c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:15:54 -0400
Subject: [PATCH 24/50] Prep release of galaxy-web-framework 20.5.0.

---
 packages/web_framework/HISTORY.rst                            | 4 ++--
 packages/web_framework/galaxy/project_galaxy_web_framework.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/web_framework/HISTORY.rst
+++ b/packages/web_framework/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py
index e6f46b22814..0b78d7933f4 100644
--- a/packages/web_framework/galaxy/project_galaxy_web_framework.py
+++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-web-framework"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 6740d3ab73923164703a0ba2b11fc0294e8ea12e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:16:28 -0400
Subject: [PATCH 25/50] Version 20.5.0 of web-framework (tag
 galaxy-web-framework-20.5.0).

---
 packages/web_framework/HISTORY.rst                            | 2 +-
 packages/web_framework/galaxy/project_galaxy_web_framework.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/web_framework/HISTORY.rst
+++ b/packages/web_framework/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py
index 0b78d7933f4..6f140273300 100644
--- a/packages/web_framework/galaxy/project_galaxy_web_framework.py
+++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-web-framework"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 479863f5feebea6c8e7b10299a1d5ab8754e6bc6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:17:12 -0400
Subject: [PATCH 26/50] Starting work on web-framework 20.5.1

---
 packages/web_framework/HISTORY.rst                          | 6 ++++++
 .../web_framework/galaxy/project_galaxy_web_framework.py    | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/web_framework/HISTORY.rst
+++ b/packages/web_framework/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py
index 6f140273300..79a5de41962 100644
--- a/packages/web_framework/galaxy/project_galaxy_web_framework.py
+++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-web-framework"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 3f828cfc6dd764bad8ccd90538b2fb7c480ceeb0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:19:53 -0400
Subject: [PATCH 27/50] Prep 20.5.0 release of galaxy-selenium.

---
 packages/selenium/HISTORY.rst                       | 4 ++--
 packages/selenium/galaxy/project_galaxy_selenium.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/selenium/HISTORY.rst
+++ b/packages/selenium/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py
index 73ec5c1cf31..b7cebadba95 100644
--- a/packages/selenium/galaxy/project_galaxy_selenium.py
+++ b/packages/selenium/galaxy/project_galaxy_selenium.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-selenium"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 06b93530a3c35b250ca6bd78df2ca96175b1d6e3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:20:12 -0400
Subject: [PATCH 28/50] Version 20.5.0 of selenium (tag
 galaxy-selenium-20.5.0).

---
 packages/selenium/HISTORY.rst                       | 2 +-
 packages/selenium/galaxy/project_galaxy_selenium.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/selenium/HISTORY.rst
+++ b/packages/selenium/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py
index b7cebadba95..8980faa0cb6 100644
--- a/packages/selenium/galaxy/project_galaxy_selenium.py
+++ b/packages/selenium/galaxy/project_galaxy_selenium.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-selenium"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From f7f04205ca15d14d16daf74b42a3c8735e7fbfd0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:20:28 -0400
Subject: [PATCH 29/50] Starting work on selenium 20.5.1

---
 packages/selenium/HISTORY.rst                       | 6 ++++++
 packages/selenium/galaxy/project_galaxy_selenium.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/selenium/HISTORY.rst
+++ b/packages/selenium/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py
index 8980faa0cb6..8682a60d8ee 100644
--- a/packages/selenium/galaxy/project_galaxy_selenium.py
+++ b/packages/selenium/galaxy/project_galaxy_selenium.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-selenium"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 8694b44d88949239e7f86fa1b754e42b76378ceb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:26:27 -0400
Subject: [PATCH 30/50] Prep release 20.5.0 of galaxy-test-base.

---
 packages/app/HISTORY.rst                              | 4 ++--
 packages/app/galaxy/project_galaxy_app.py             | 2 +-
 packages/test_base/HISTORY.rst                        | 4 ++--
 packages/test_base/galaxy/project_galaxy_test_base.py | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/app/HISTORY.rst
+++ b/packages/app/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
index 95cac65f339..12e2f71311c 100644
--- a/packages/app/galaxy/project_galaxy_app.py
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-app"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
index 7cb67f838f8..de8bcfa7be3 100644
--- a/packages/test_base/HISTORY.rst
+++ b/packages/test_base/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.1.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 20.01 development cycle.
+* Initial import from the 20.05 branch of Galaxy.
diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py
index 668485b359f..9e6dd6c09e1 100644
--- a/packages/test_base/galaxy/project_galaxy_test_base.py
+++ b/packages/test_base/galaxy/project_galaxy_test_base.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.1.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-test-base"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 55beabf25a91e9363e9acbe773ca803e4c557409 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:26:59 -0400
Subject: [PATCH 31/50] Version 20.5.0 of test-base (tag
 galaxy-test-base-20.5.0).

---
 packages/test_base/HISTORY.rst                        | 2 +-
 packages/test_base/galaxy/project_galaxy_test_base.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
index de8bcfa7be3..16731e203d2 100644
--- a/packages/test_base/HISTORY.rst
+++ b/packages/test_base/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * Initial import from the 20.05 branch of Galaxy.
diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py
index 9e6dd6c09e1..a7ec2da566a 100644
--- a/packages/test_base/galaxy/project_galaxy_test_base.py
+++ b/packages/test_base/galaxy/project_galaxy_test_base.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-test-base"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 3850e736cdea413de271628a53be2c592fb806b8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 10:27:43 -0400
Subject: [PATCH 32/50] Starting work on test-base 20.5.1

---
 packages/test_base/HISTORY.rst                        | 6 ++++++
 packages/test_base/galaxy/project_galaxy_test_base.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst
index 16731e203d2..b8a2e6045e6 100644
--- a/packages/test_base/HISTORY.rst
+++ b/packages/test_base/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py
index a7ec2da566a..d2ae57543f9 100644
--- a/packages/test_base/galaxy/project_galaxy_test_base.py
+++ b/packages/test_base/galaxy/project_galaxy_test_base.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-test-base"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 4e845985d32b423106a31eae711b702cffea1df6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:42:13 -0400
Subject: [PATCH 33/50] Version 20.5.0 of app (tag galaxy-app-20.5.0).

---
 packages/app/HISTORY.rst                  | 2 +-
 packages/app/galaxy/project_galaxy_app.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/app/HISTORY.rst
+++ b/packages/app/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
index 12e2f71311c..078f7583813 100644
--- a/packages/app/galaxy/project_galaxy_app.py
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-app"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From e2620bd578b284f22884ac2e8c15f6d53c8bcc98 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:42:46 -0400
Subject: [PATCH 34/50] Starting work on app 20.5.1

---
 packages/app/HISTORY.rst                  | 6 ++++++
 packages/app/galaxy/project_galaxy_app.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/app/HISTORY.rst
+++ b/packages/app/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
index 078f7583813..61a6ae88785 100644
--- a/packages/app/galaxy/project_galaxy_app.py
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-app"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From be323a369fd4eb9b768bfd3b3b73b53d9d42efa7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:44:21 -0400
Subject: [PATCH 35/50] Prep release of galaxy-web-apps 20.5.0.

---
 packages/web_apps/HISTORY.rst                       | 4 ++--
 packages/web_apps/galaxy/project_galaxy_web_apps.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
index ec2f0e746e9..75fa1f7b125 100644
--- a/packages/web_apps/HISTORY.rst
+++ b/packages/web_apps/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-19.9.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 19.09 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_apps/galaxy/project_galaxy_web_apps.py b/packages/web_apps/galaxy/project_galaxy_web_apps.py
index 3f416bde726..ef2b4f3bbf6 100644
--- a/packages/web_apps/galaxy/project_galaxy_web_apps.py
+++ b/packages/web_apps/galaxy/project_galaxy_web_apps.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '19.9.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-web-apps"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 29e4fc84660a53a407fa77f15142448e68a448af Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:44:35 -0400
Subject: [PATCH 36/50] Version 20.5.0 of web-apps (tag
 galaxy-web-apps-20.5.0).

---
 packages/web_apps/HISTORY.rst                       | 2 +-
 packages/web_apps/galaxy/project_galaxy_web_apps.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/web_apps/HISTORY.rst
+++ b/packages/web_apps/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/web_apps/galaxy/project_galaxy_web_apps.py b/packages/web_apps/galaxy/project_galaxy_web_apps.py
index ef2b4f3bbf6..6ffb321532f 100644
--- a/packages/web_apps/galaxy/project_galaxy_web_apps.py
+++ b/packages/web_apps/galaxy/project_galaxy_web_apps.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-web-apps"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 9531a54fa9dd798088dd9e19d15cdf3bc393dfa0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:45:04 -0400
Subject: [PATCH 37/50] Starting work on web-apps 20.5.1

---
 packages/web_apps/HISTORY.rst                       | 6 ++++++
 packages/web_apps/galaxy/project_galaxy_web_apps.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/web_apps/HISTORY.rst
+++ b/packages/web_apps/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/web_apps/galaxy/project_galaxy_web_apps.py b/packages/web_apps/galaxy/project_galaxy_web_apps.py
index 6ffb321532f..0ba5f8b7ee8 100644
--- a/packages/web_apps/galaxy/project_galaxy_web_apps.py
+++ b/packages/web_apps/galaxy/project_galaxy_web_apps.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-web-apps"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 7d01e41a52f197a8367cce9f28301ff328887505 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:46:26 -0400
Subject: [PATCH 38/50] Prep release of galaxy-test-driver 20.5.0.

---
 packages/test_driver/HISTORY.rst                          | 4 ++--
 packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
index 7cb67f838f8..75fa1f7b125 100644
--- a/packages/test_driver/HISTORY.rst
+++ b/packages/test_driver/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.1.0.dev0
+20.5.0.dev0
 ---------------------
 
-* Initial import from dev branch of Galaxy during 20.01 development cycle.
+* First release from the 20.05 branch of Galaxy.
diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py
index 3c665e4adfb..eebf0650f71 100644
--- a/packages/test_driver/galaxy/project_galaxy_test_driver.py
+++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.1.0.dev0'
+__version__ = '20.5.0.dev0'
 
 PROJECT_NAME = "galaxy-test-driver"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From d266bee81d598415f98e900230aa80ad64f1743e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:46:37 -0400
Subject: [PATCH 39/50] Version 20.5.0 of test-driver (tag
 galaxy-test-driver-20.5.0).

---
 packages/test_driver/HISTORY.rst                          | 2 +-
 packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
index 75fa1f7b125..0de170a85ca 100644
--- a/packages/test_driver/HISTORY.rst
+++ b/packages/test_driver/HISTORY.rst
@@ -6,7 +6,7 @@ History
 .. to_doc
 
 ---------------------
-20.5.0.dev0
+20.5.0 (2020-07-04)
 ---------------------
 
 * First release from the 20.05 branch of Galaxy.
diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py
index eebf0650f71..5506d48d180 100644
--- a/packages/test_driver/galaxy/project_galaxy_test_driver.py
+++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0.dev0'
+__version__ = '20.5.0'
 
 PROJECT_NAME = "galaxy-test-driver"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 28ac609b43c979c013eca6fa2a406786b6893860 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 4 Jul 2020 11:46:51 -0400
Subject: [PATCH 40/50] Starting work on test-driver 20.5.1

---
 packages/test_driver/HISTORY.rst                          | 6 ++++++
 packages/test_driver/galaxy/project_galaxy_test_driver.py | 2 +-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst
index 0de170a85ca..72090ac4c88 100644
--- a/packages/test_driver/HISTORY.rst
+++ b/packages/test_driver/HISTORY.rst
@@ -5,6 +5,12 @@ History
 
 .. to_doc
 
+---------------------
+20.5.1.dev0
+---------------------
+
+
+
 ---------------------
 20.5.0 (2020-07-04)
 ---------------------
diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py
index 5506d48d180..ccf9c1596b8 100644
--- a/packages/test_driver/galaxy/project_galaxy_test_driver.py
+++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '20.5.0'
+__version__ = '20.5.1.dev0'
 
 PROJECT_NAME = "galaxy-test-driver"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 0c78aca542ab544e82897aa3e0249dfb8146c11e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 19:16:35 +0200
Subject: [PATCH 41/50] Allow setting metadata_strategy per destination

This allows instances that mix classic job runners with pulsar to use
metadata_strategy: extended on destinations that are not served by
pulsar.
---
 lib/galaxy/jobs/__init__.py                            | 10 +++++-----
 test/integration/embedded_pulsar_metadata_job_conf.yml |  1 +
 test/integration/test_pulsar_embedded_metadata.py      |  4 ++++
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 4c882990f58..ad4cf4fde23 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -906,17 +906,17 @@ class JobWrapper(HasResourceParameters):
         self.output_paths = None
         self.output_hdas_and_paths = None
         self.tool_provided_job_metadata = None
-        # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        metadata_strategy_override = None
-        if job.tasks:
-            metadata_strategy_override = "directory"
-        self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id, metadata_strategy_override=metadata_strategy_override)
         self.job_runner_mapper = JobRunnerMapper(self, queue.dispatcher.url_to_destination, self.app.job_config)
         self.params = None
         if job.params:
             self.params = loads(job.params)
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)
+        # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
+        metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+        if job.tasks:
+            metadata_strategy_override = "directory"
+        self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id, metadata_strategy_override=metadata_strategy_override)
 
         self.__commands_in_new_shell = True
         self.__user_system_pwent = None
diff --git a/test/integration/embedded_pulsar_metadata_job_conf.yml b/test/integration/embedded_pulsar_metadata_job_conf.yml
index 76520bf4ed5..451162866a0 100644
--- a/test/integration/embedded_pulsar_metadata_job_conf.yml
+++ b/test/integration/embedded_pulsar_metadata_job_conf.yml
@@ -13,6 +13,7 @@ execution:
       runner: pulsar_embed
       remote_metadata: true
       default_file_action: copy
+      metadata_strategy: directory
 
 tools:
 - id: upload1
diff --git a/test/integration/test_pulsar_embedded_metadata.py b/test/integration/test_pulsar_embedded_metadata.py
index 4ebae4a5037..14dc616281d 100644
--- a/test/integration/test_pulsar_embedded_metadata.py
+++ b/test/integration/test_pulsar_embedded_metadata.py
@@ -16,6 +16,10 @@ class EmbeddedMetadataPulsarIntegrationInstance(integration_util.IntegrationInst
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
+        config['object_store_store_by'] = 'uuid'
+        # metadata_strategy is being set to directory in embedded_pulsar_metadata_job_conf.yml,
+        # since extended_metadata doesn't work yet on pulsar
+        config['metadata_strategy'] = 'extended'
 
 
 instance = integration_util.integration_module_instance(EmbeddedMetadataPulsarIntegrationInstance)

From ea3f48a5ec1220a1d1d0b614cbb66cbdeebaa79d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 19:41:11 +0200
Subject: [PATCH 42/50] Document metadata_strategy

---
 doc/source/admin/galaxy_options.rst              | 16 ++++++++++++++++
 lib/galaxy/config/sample/galaxy.yml.sample       |  9 +++++++++
 .../config/sample/job_conf.xml.sample_advanced   | 11 +++++++++++
 lib/galaxy/webapps/galaxy/config_schema.yml      | 12 ++++++++++++
 4 files changed, 48 insertions(+)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 40defa60e8a..1682b35b062 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3563,6 +3563,22 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~
+``metadata_strategy``
+~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Determines how metadata will be set. Valid values are `directory`,
+    `extended` and `legacy`. In extended mode jobs will decide if a
+    tool run failed, the object stores  configuration is serialized
+    and made available to the job and is used for writing output
+    datasets to the  object store as part of the job and dynamic
+    output discovery (e.g. discovered datasets <discover_datasets>,
+    unpopulated collections, etc) happens as part of the job.
+:Default: ``directory``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``retry_metadata_internally``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 1fe69acef2a..c28ab6fab5b 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1741,6 +1741,15 @@ galaxy:
   # database.
   #enable_job_recovery: true
 
+  # Determines how metadata will be set. Valid values are `directory`,
+  # `extended` and `legacy`. In extended mode jobs will decide if a tool
+  # run failed, the object stores  configuration is serialized and made
+  # available to the job and is used for writing output datasets to the
+  # object store as part of the job and dynamic output discovery (e.g.
+  # discovered datasets <discover_datasets>, unpopulated collections,
+  # etc) happens as part of the job.
+  #metadata_strategy: directory
+
   # Although it is fairly reliable, setting metadata can occasionally
   # fail.  In these instances, you can choose to retry setting it
   # internally or leave it in a failed state (since retrying internally
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index 53254618eba..f44a940a95e 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -401,6 +401,17 @@
                try it early - it will slightly speed up local jobs by
                embedding metadata calculation in job script itself.
           -->
+          <param id="metadata_strategy">directory</param>
+          <!-- If set overwrites metadata_strategy (configurable in galaxy.yml).
+               Valid values are `directory` (default), `extended` and `legacy`.
+               Setting metadata_strategy to extended requires that all object stores
+               that can be written to store datasets by uuid. In extended mode jobs
+               will decide if a tool run failed, the object stores configuration
+               is serialized and made available to the job and is used for writing output
+               datasets to the object store as part of the job and dynamic output discovery
+               (e.g. discovered datasets <discover_datasets>, unpopulated collections, etc)
+               happens as part of the job.
+          -->
           <job_metrics />
           <!-- Above element demonstrates embedded job metrics definition - see
                job_metrics_conf.xml.sample for full documentation on possible nested
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 3e45d43fcbd..df648f396c3 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2638,6 +2638,18 @@ mapping:
           it can "recover" them when it starts).  This is not safe to use if you are
           running more than one Galaxy server using the same database.
 
+      metadata_strategy:
+        type: str
+        required: false
+        default: directory
+        desc: |
+          Determines how metadata will be set. Valid values are `directory`, `extended` and `legacy`.
+          In extended mode jobs will decide if a tool run failed, the object stores
+          configuration is serialized and made available to the job and is used for
+          writing output datasets to the  object store as part of the job and dynamic
+          output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
+          etc) happens as part of the job.
+
       retry_metadata_internally:
         type: bool
         default: true

From 3efbfc83e3c667a0ddc26af2455f4750743bf6b7 Mon Sep 17 00:00:00 2001
From: Nolan Woods <nolan_w@sfu.ca>
Date: Sat, 4 Jul 2020 11:24:47 -0700
Subject: [PATCH 43/50] Update pysam to 0.16.0.1

---
 .../dependencies/pipfiles/default/pinned-requirements.txt       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
index e98273ceaad..fec4f6d9601 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
@@ -138,7 +138,7 @@ pyopenssl==19.1.0
 pyparsing==2.4.7
 pyperclip==1.8.0
 pyrsistent==0.16.0
-pysam==0.15.4
+pysam==0.16.0.1
 pysftp==0.2.9
 python-cinderclient==4.0.0
 python-dateutil==2.8.1

From ef089655014846c08ba7b7db42b49bd8d673f3b3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 20:58:01 +0200
Subject: [PATCH 44/50] Doc and comment fixes

---
 doc/source/admin/galaxy_options.rst                   | 8 ++++----
 lib/galaxy/config/sample/galaxy.yml.sample            | 2 +-
 lib/galaxy/config/sample/job_conf.xml.sample_advanced | 6 +++---
 lib/galaxy/webapps/galaxy/config_schema.yml           | 2 +-
 test/integration/test_pulsar_embedded_metadata.py     | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 1682b35b062..ebc6824d962 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -3570,10 +3570,10 @@
 :Description:
     Determines how metadata will be set. Valid values are `directory`,
     `extended` and `legacy`. In extended mode jobs will decide if a
-    tool run failed, the object stores  configuration is serialized
-    and made available to the job and is used for writing output
-    datasets to the  object store as part of the job and dynamic
-    output discovery (e.g. discovered datasets <discover_datasets>,
+    tool run failed, the object stores configuration is serialized and
+    made available to the job and is used for writing output datasets
+    to the object store as part of the job and dynamic output
+    discovery (e.g. discovered datasets <discover_datasets>,
     unpopulated collections, etc) happens as part of the job.
 :Default: ``directory``
 :Type: str
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index c28ab6fab5b..f14fd7cafe9 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -1743,7 +1743,7 @@ galaxy:
 
   # Determines how metadata will be set. Valid values are `directory`,
   # `extended` and `legacy`. In extended mode jobs will decide if a tool
-  # run failed, the object stores  configuration is serialized and made
+  # run failed, the object stores configuration is serialized and made
   # available to the job and is used for writing output datasets to the
   # object store as part of the job and dynamic output discovery (e.g.
   # discovered datasets <discover_datasets>, unpopulated collections,
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index f44a940a95e..beb5feb3d13 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -402,10 +402,10 @@
                embedding metadata calculation in job script itself.
           -->
           <param id="metadata_strategy">directory</param>
-          <!-- If set overwrites metadata_strategy (configurable in galaxy.yml).
+          <!-- If set, overwrites metadata_strategy (configurable in galaxy.yml).
                Valid values are `directory` (default), `extended` and `legacy`.
-               Setting metadata_strategy to extended requires that all object stores
-               that can be written to store datasets by uuid. In extended mode jobs
+               Setting metadata_strategy to `extended` requires that all object stores
+               that can be written to store datasets by uuid. In `extended` mode jobs
                will decide if a tool run failed, the object stores configuration
                is serialized and made available to the job and is used for writing output
                datasets to the object store as part of the job and dynamic output discovery
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index df648f396c3..1eaa2a7f909 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -2646,7 +2646,7 @@ mapping:
           Determines how metadata will be set. Valid values are `directory`, `extended` and `legacy`.
           In extended mode jobs will decide if a tool run failed, the object stores
           configuration is serialized and made available to the job and is used for
-          writing output datasets to the  object store as part of the job and dynamic
+          writing output datasets to the object store as part of the job and dynamic
           output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
           etc) happens as part of the job.
 
diff --git a/test/integration/test_pulsar_embedded_metadata.py b/test/integration/test_pulsar_embedded_metadata.py
index 14dc616281d..cd59298a45d 100644
--- a/test/integration/test_pulsar_embedded_metadata.py
+++ b/test/integration/test_pulsar_embedded_metadata.py
@@ -17,8 +17,8 @@ class EmbeddedMetadataPulsarIntegrationInstance(integration_util.IntegrationInst
     def handle_galaxy_config_kwds(cls, config):
         config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
         config['object_store_store_by'] = 'uuid'
-        # metadata_strategy is being set to directory in embedded_pulsar_metadata_job_conf.yml,
-        # since extended_metadata doesn't work yet on pulsar
+        # We set the global metadata_strategy to `extended, but`metadata_strategy is
+        # being overridden in embedded_pulsar_metadata_job_conf.yml, since extended_metadata does not yet work on pulsar
         config['metadata_strategy'] = 'extended'
 
 

From a3080bb53d239c4480f4658f1035cc154a0a6d22 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 23:05:19 +0200
Subject: [PATCH 45/50] Use default metadata_strategy of job can't be mapped

---
 lib/galaxy/jobs/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index ad4cf4fde23..cfea0af1249 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -913,7 +913,10 @@ class JobWrapper(HasResourceParameters):
         if use_persisted_destination:
             self.job_runner_mapper.cached_job_destination = JobDestination(from_job=job)
         # Wrapper holding the info required to restore and clean up from files used for setting metadata externally
-        metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+        try:
+            metadata_strategy_override = self.get_destination_configuration('metadata_strategy', None)
+        except JobMappingException:
+            metadata_strategy_override = None
         if job.tasks:
             metadata_strategy_override = "directory"
         self.external_output_metadata = get_metadata_compute_strategy(self.app.config, job.id, metadata_strategy_override=metadata_strategy_override)

From f50a02078ab48c55471577c12064aa1bfa9ce97f Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 8 Jul 2020 16:41:32 +0200
Subject: [PATCH 46/50] Import MetadataFile in extended_metadata mode

We used to skip MetadaFile, despite it being generated and pushed to the
object store. And we need to allow MetadataFile as a marshalled value
when there is no associated ID yet.
Should fix
```
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: Traceback (most recent call last):
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/server/lib/galaxy/jobs/runners/pulsar.py", line 390, in queue_job
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: job_id = pulsar_submit_job(client, client_job_description, remote_job_config)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 27, in submit_job
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: file_stager = FileStager(client, client_job_description, job_config)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 123, in __init__
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: self.__upload_input_files()
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 236, in __upload_input_files
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: self.__upload_input_metadata_file(client_input.action_source)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 255, in __upload_input_metadata_file
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: self.transfer_tracker.handle_transfer_source(input_action_source, path_type.INPUT, name=remote_name)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 462, in handle_transfer_source
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: action = self.__action_for_transfer(source, type, contents)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: File "/opt/galaxy/venv/lib/python3.6/site-packages/pulsar/client/staging/up.py", line 518, in __action_for_transfer
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: raise Exception(message)
Jul 08 11:25:23 test.internal.usegalaxy.eu.novalocal python[873067]: Exception: __action_for_transfer called on non-existent file - [None]
```

reported in https://github.com/galaxyproject/galaxy/issues/9968
---
 lib/galaxy/metadata/set_metadata.py | 2 +-
 lib/galaxy/model/metadata.py        | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index 5724c5543d2..c8077132cc4 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -174,7 +174,7 @@ def set_metadata_portable():
 
         # Load outputs.
         import_model_store = store.imported_store_for_metadata('metadata/outputs_new', object_store=object_store)
-        export_store = store.DirectoryModelExportStore('metadata/outputs_populated', serialize_dataset_objects=True, for_edit=True)
+        export_store = store.DirectoryModelExportStore('metadata/outputs_populated', serialize_dataset_objects=True, for_edit=True, strip_metadata_files=False)
 
     for output_name, output_dict in outputs.items():
         if extended_metadata_collection:
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index c257e2960e4..0bbc87eeb4c 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -524,8 +524,7 @@ class FileParameter(MetadataParameter):
             return None
         if isinstance(value, galaxy.model.MetadataFile) or isinstance(value, MetadataTempFile):
             return value
-        mf = session.query(galaxy.model.MetadataFile).get(value)
-        return mf
+        return session.query(galaxy.model.MetadataFile).get(value)
 
     def make_copy(self, value, target_context, source_context):
         value = self.wrap(value, object_session(target_context.parent))
@@ -540,7 +539,10 @@ class FileParameter(MetadataParameter):
     @classmethod
     def marshal(cls, value):
         if isinstance(value, galaxy.model.MetadataFile):
-            value = value.id
+            # We want to push value.id to the database, but need to skip this when no session is available,
+            # as in extended_metadata mode, so there we just accept MetadataFile.
+            # We will only serialize MetadataFile in this mode and not push to the database, so this is OK.
+            value = value.id or value
         return value
 
     def from_external_value(self, value, parent, path_rewriter=None):

From a6aa1c932e7780228405c6d3e87d104e1c08dd25 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 9 Jul 2020 12:09:11 +0200
Subject: [PATCH 47/50] Extend pulsar metadata testing to cover MetadataFile
 inputs

---
 test/functional/tools/metadata_bam.xml            | 5 +++--
 test/integration/test_pulsar_embedded_metadata.py | 3 ++-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/test/functional/tools/metadata_bam.xml b/test/functional/tools/metadata_bam.xml
index 2f20be5b531..6ee6bfa417c 100644
--- a/test/functional/tools/metadata_bam.xml
+++ b/test/functional/tools/metadata_bam.xml
@@ -1,5 +1,6 @@
-<tool id="metadata_bam" name="metadata BAM" version="1.0.0">
-  <command>echo "${ref_names}" &gt; "${output_of_input_metadata}"</command>
+<tool id="metadata_bam" name="metadata BAM" version="1.0.0" profile="16.04">
+  <command><![CDATA[ #assert $input_bam.metadata.bam_index
+echo "${ref_names}" > "${output_of_input_metadata}"]]></command>
   <inputs>
     <param name="input_bam" type="data" format="bam" label="BAM File"/>
     <param name="ref_names" type="select" optional="False" label="Select references you would like to restrict bam to" multiple="True">
diff --git a/test/integration/test_pulsar_embedded_metadata.py b/test/integration/test_pulsar_embedded_metadata.py
index cd59298a45d..4ba5a600c7d 100644
--- a/test/integration/test_pulsar_embedded_metadata.py
+++ b/test/integration/test_pulsar_embedded_metadata.py
@@ -20,8 +20,9 @@ class EmbeddedMetadataPulsarIntegrationInstance(integration_util.IntegrationInst
         # We set the global metadata_strategy to `extended, but`metadata_strategy is
         # being overridden in embedded_pulsar_metadata_job_conf.yml, since extended_metadata does not yet work on pulsar
         config['metadata_strategy'] = 'extended'
+        config['retry_metadata_internally'] = False
 
 
 instance = integration_util.integration_module_instance(EmbeddedMetadataPulsarIntegrationInstance)
 
-test_tools = integration_util.integration_tool_runner(["simple_constructs"])
+test_tools = integration_util.integration_tool_runner(["simple_constructs", "metadata_bam"])

From 6648890328521dbc8896c9000f8c0616f42587b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 9 Jul 2020 15:21:43 +0200
Subject: [PATCH 48/50] Update test/functional/tools/metadata_bam.xml

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 test/functional/tools/metadata_bam.xml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/functional/tools/metadata_bam.xml b/test/functional/tools/metadata_bam.xml
index 6ee6bfa417c..6cf73b2e9c3 100644
--- a/test/functional/tools/metadata_bam.xml
+++ b/test/functional/tools/metadata_bam.xml
@@ -1,6 +1,8 @@
 <tool id="metadata_bam" name="metadata BAM" version="1.0.0" profile="16.04">
-  <command><![CDATA[ #assert $input_bam.metadata.bam_index
-echo "${ref_names}" > "${output_of_input_metadata}"]]></command>
+  <command><![CDATA[
+#assert $input_bam.metadata.bam_index
+echo '${ref_names}' > '${output_of_input_metadata}'
+  ]]></command>
   <inputs>
     <param name="input_bam" type="data" format="bam" label="BAM File"/>
     <param name="ref_names" type="select" optional="False" label="Select references you would like to restrict bam to" multiple="True">

From ae2bf3c357486ff49c4742e3e92ed0100a47c3bc Mon Sep 17 00:00:00 2001
From: almahmoud <amahmou4@jhu.edu>
Date: Mon, 13 Jul 2020 17:51:27 -0400
Subject: [PATCH 49/50] Change cookie names to work with PR #9921

---
 lib/galaxy/authnz/custos_authnz.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/authnz/custos_authnz.py b/lib/galaxy/authnz/custos_authnz.py
index 165f6a5615a..bcd982b2abc 100644
--- a/lib/galaxy/authnz/custos_authnz.py
+++ b/lib/galaxy/authnz/custos_authnz.py
@@ -16,8 +16,8 @@ from galaxy.model import CustosAuthnzToken, User
 from ..authnz import IdentityProvider
 
 log = logging.getLogger(__name__)
-STATE_COOKIE_NAME = 'custos-state'
-NONCE_COOKIE_NAME = 'custos-nonce'
+STATE_COOKIE_NAME = 'galaxy-oidc-state'
+NONCE_COOKIE_NAME = 'galaxy-oidc-nonce'
 
 
 class CustosAuthnz(IdentityProvider):

From 3e6efc70fd5fbb74eb1c8336fae3a6f699e637d7 Mon Sep 17 00:00:00 2001
From: almahmoud <amahmou4@jhu.edu>
Date: Mon, 13 Jul 2020 17:55:21 -0400
Subject: [PATCH 50/50] Replace e.message with str(e) for Python 3
 compatibility

---
 lib/galaxy/authnz/managers.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/authnz/managers.py b/lib/galaxy/authnz/managers.py
index 1876bdb82bd..38f9ceaf4a3 100644
--- a/lib/galaxy/authnz/managers.py
+++ b/lib/galaxy/authnz/managers.py
@@ -260,7 +260,7 @@ class AuthnzManager(object):
             return True, message, backend.callback(state_token, authz_code, trans, login_redirect_url)
         except Exception as e:
             msg = 'The following error occurred when handling callback from `{}` identity provider: ' \
-                  '{}'.format(provider, e.message)
+                  '{}'.format(provider, str(e))
             log.exception(msg)
             return False, msg, (None, None)
 
@@ -289,7 +289,7 @@ class AuthnzManager(object):
             return True, message, backend.logout(trans, post_logout_redirect_url)
         except Exception as e:
             msg = 'The following error occurred when logging out from `{}` identity provider: ' \
-                  '{}'.format(provider, e.message)
+                  '{}'.format(provider, str(e))
             log.exception(msg)
             return False, msg, None