From 10ef0a3b00681dbab09119cc057a3ebe47e3d4f9 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Apr 2016 17:48:15 +0200
Subject: [PATCH 1/6] HTCondor and Docker documentation

---
 config/job_conf.xml.sample_advanced | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 92dbe4e3410..217a6a07f33 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -434,6 +434,25 @@
                  <param> tags.
             -->
             <param id="request_cpus">8</param>
+
+            <!-- Recent version of HTCondor do have a `docker` universe to handle containers.
+                 Activate this feature by explicitly specifying the `docker` universe.
+            -->
+            <!-- <param id="universe">docker</param> -->
+
+            <!-- If the tool has a container specified this one is used.
+
+                <requirements>
+                    <container type="docker">bgruening/galaxy-stable</container>
+                </requirements>
+
+                If not the container specified with id="docker_image" is used and as last resort
+                id="docker_default_container_id" is considered.
+            -->
+
+            <!-- <param id="docker_image">busybox:ubuntu-14.04</param> -->
+            <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
+
         </destination>
 
         <!-- Jobs that hit the walltime on one destination can be automatically

From ba409e75181224c80f0acf02530cac31fe28461c Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Apr 2016 17:50:33 +0200
Subject: [PATCH 2/6] enable HTCondor Docker integration

---
 lib/galaxy/jobs/runners/condor.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/lib/galaxy/jobs/runners/condor.py b/lib/galaxy/jobs/runners/condor.py
index 97e9cab6ebc..4b2011bf32c 100644
--- a/lib/galaxy/jobs/runners/condor.py
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -57,6 +57,19 @@ class CondorJobRunner( AsynchronousJobRunner ):
 
         # get destination params
         query_params = submission_params(prefix="", **job_destination.params)
+        container = None
+        universe = query_params.get('universe', False)
+        if universe.strip().lower() == 'docker':
+            if job_wrapper.tool.containers:
+                # Try to extract the container (1) from the Tool, (2) from 'docker_image'
+                # and (3) from 'docker_default_container_id'. The last two can be specified in job_conf.xml
+                container = job_wrapper.tool.containers[0].identifier or \
+                    query_params.get('docker_image', False) or \
+                    query_params.get('docker_default_container_id', False)
+            if container:
+                # HTCondor needs the image as 'docker_image'
+                query_params.update({'docker_image': container})
+
         galaxy_slots = query_params.get('request_cpus', None)
         if galaxy_slots:
             galaxy_slots_statement = 'GALAXY_SLOTS="%s"; export GALAXY_SLOTS_CONFIGURED="1"' % galaxy_slots

From 3ab43e38f5b2d63c300e99635234051956905f94 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Apr 2016 19:12:32 +0200
Subject: [PATCH 3/6] add new Docker Image. We need to have bash inside of
 Docker.

---
 test/functional/tools/catDocker.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/functional/tools/catDocker.xml b/test/functional/tools/catDocker.xml
index 1437ebb717b..d249728a7ec 100644
--- a/test/functional/tools/catDocker.xml
+++ b/test/functional/tools/catDocker.xml
@@ -1,9 +1,9 @@
 <tool id="catdc" name="Concatenate datasets (in docker)">
     <description>tail-to-head</description>
     <requirements>
-      <container type="docker">busybox:ubuntu-14.04</container>
+      <container type="docker">bgruening/busybox-bash:0.1</container>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
       echo "Galaxy slots passed through contain as \$GALAXY_SLOTS";
       cat $input1
       #for $q in $queries

From ead96a55a9d05602a7b241d2d8b8acf557ce9425 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sun, 1 May 2016 14:14:32 +0200
Subject: [PATCH 4/6] Add the ability to set the default handler and
 destination via environment variables.

---
 lib/galaxy/jobs/__init__.py | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 137e81f0b6b..febe00e05bc 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -413,7 +413,15 @@ class JobConfiguration( object ):
 
         :returns: str -- id or tag representing the default.
         """
+
         rval = parent.get('default')
+        if 'default_from_environ' in parent.attrib:
+            environ_var = parent.attrib['default_from_environ']
+            rval = os.environ.get(environ_var, rval)
+        elif 'default_from_config' in parent.attrib:
+            config_val = parent.attrib['default_from_config']
+            rval = self.app.config.config_dict.get(config_val, rval)
+
         if rval is not None:
             # If the parent element has a 'default' attribute, use the id or tag in that attribute
             if rval not in names:

From 7bd595b8f1caf4ea5085a41ba8129653d48f83a7 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Mon, 2 May 2016 15:25:13 +0200
Subject: [PATCH 5/6] Revert "add new Docker Image. We need to have bash inside
 of Docker."

This reverts commit 3ab43e38f5b2d63c300e99635234051956905f94.
---
 test/functional/tools/catDocker.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/functional/tools/catDocker.xml b/test/functional/tools/catDocker.xml
index d249728a7ec..1437ebb717b 100644
--- a/test/functional/tools/catDocker.xml
+++ b/test/functional/tools/catDocker.xml
@@ -1,9 +1,9 @@
 <tool id="catdc" name="Concatenate datasets (in docker)">
     <description>tail-to-head</description>
     <requirements>
-      <container type="docker">bgruening/busybox-bash:0.1</container>
+      <container type="docker">busybox:ubuntu-14.04</container>
     </requirements>
-    <command detect_errors="exit_code">
+    <command>
       echo "Galaxy slots passed through contain as \$GALAXY_SLOTS";
       cat $input1
       #for $q in $queries

From 917c882255ff1261bb99bb4bfc8bd1e165e26b96 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 16 May 2016 14:52:21 -0400
Subject: [PATCH 6/6] Revise HTCondor Docker image resolution.

Bring inline with the rest of the job runner's Docker image resolution stuff. Order of reosolution is:

 - Use destination specified override if found: docker_container_id_override
 - Use the tool specified container if not found and no override: see tool
 - Else - use docker_default_container_id.

This adjusts the documentation to reflect this and make the the parameters more consistent throughout. I've modified this so docker_image (the old name introduced by the Docker Condor PR) still works - but I have left it undocumented intentionally for consistency.
---
 config/job_conf.xml.sample_advanced | 11 ++++++-----
 lib/galaxy/jobs/runners/condor.py   |  7 +------
 lib/galaxy/tools/deps/containers.py |  6 +++++-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/config/job_conf.xml.sample_advanced b/config/job_conf.xml.sample_advanced
index 217a6a07f33..7d94947a921 100644
--- a/config/job_conf.xml.sample_advanced
+++ b/config/job_conf.xml.sample_advanced
@@ -446,13 +446,14 @@
                     <container type="docker">bgruening/galaxy-stable</container>
                 </requirements>
 
-                If not the container specified with id="docker_image" is used and as last resort
-                id="docker_default_container_id" is considered.
+            Unless the job destination specifies an override 
+            with docker_container_id_override. If neither of 
+            these is set a default container can be specified
+            with docker_default_container_id. The resolved
+            container ID will be passed along to condor as
+            the docker_image submission parameter.
             -->
-
-            <!-- <param id="docker_image">busybox:ubuntu-14.04</param> -->
             <!-- <param id="docker_default_container_id">busybox:ubuntu-14.04</param> -->
-
         </destination>
 
         <!-- Jobs that hit the walltime on one destination can be automatically
diff --git a/lib/galaxy/jobs/runners/condor.py b/lib/galaxy/jobs/runners/condor.py
index 4b2011bf32c..f25b7676a66 100644
--- a/lib/galaxy/jobs/runners/condor.py
+++ b/lib/galaxy/jobs/runners/condor.py
@@ -60,12 +60,7 @@ class CondorJobRunner( AsynchronousJobRunner ):
         container = None
         universe = query_params.get('universe', False)
         if universe.strip().lower() == 'docker':
-            if job_wrapper.tool.containers:
-                # Try to extract the container (1) from the Tool, (2) from 'docker_image'
-                # and (3) from 'docker_default_container_id'. The last two can be specified in job_conf.xml
-                container = job_wrapper.tool.containers[0].identifier or \
-                    query_params.get('docker_image', False) or \
-                    query_params.get('docker_default_container_id', False)
+            container = self.find_container( job_wrapper )
             if container:
                 # HTCondor needs the image as 'docker_image'
                 query_params.update({'docker_image': container})
diff --git a/lib/galaxy/tools/deps/containers.py b/lib/galaxy/tools/deps/containers.py
index 12b2f3c879e..948c5b851b4 100644
--- a/lib/galaxy/tools/deps/containers.py
+++ b/lib/galaxy/tools/deps/containers.py
@@ -107,7 +107,11 @@ class ContainerFinder(object):
     def __default_container_id(self, container_type, destination_info):
         if not self.__container_type_enabled(container_type, destination_info):
             return None
-        return destination_info.get("%s_default_container_id" % container_type)
+        key = "%s_default_container_id" % container_type
+        # Also allow docker_image...
+        if key not in destination_info:
+            key = "%s_image" % container_type
+        return destination_info.get(key)
 
     def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info):
         # TODO: ensure destination_info is dict-like