From e1f517cf4b74ad8b3882b965caecda127c4b1773 Mon Sep 17 00:00:00 2001
From: almahmoud <amahmou4@jhu.edu>
Date: Wed, 12 May 2021 13:34:39 -0400
Subject: [PATCH] Remove separate conf files

---
 config/galaxy.yml.k8s_interactivetools        | 20 ---------
 config/job_conf.yml.k8s_interactivetools      | 41 -------------------
 .../sample/job_conf.xml.sample_advanced       | 14 +++++++
 3 files changed, 14 insertions(+), 61 deletions(-)
 delete mode 100644 config/galaxy.yml.k8s_interactivetools
 delete mode 100644 config/job_conf.yml.k8s_interactivetools

diff --git a/config/galaxy.yml.k8s_interactivetools b/config/galaxy.yml.k8s_interactivetools
deleted file mode 100644
index 46d03989062..00000000000
--- a/config/galaxy.yml.k8s_interactivetools
+++ /dev/null
@@ -1,20 +0,0 @@
-galaxy:
-  conda_auto_init: false
-  enable_data_manager_user_view: true
-  enable_tool_document_cache: true
-  integrated_tool_panel_config: /galaxy/server/config/mutable/integrated_tool_panel.xml
-  interactivetools_enable: true
-  interactivetools_map: database/interactivetools_map.sqlite
-  interactivetools_prefix: "its"
-  interactivetools_proxy_host: my-galaxy.usegvl.org
-  interactivetools_shorten_url: true
-  nginx_x_accel_redirect_base: '/galaxy/_x_accel_redirect'
-  outputs_to_working_directory: true
-  sanitize_allowlist_file: /galaxy/server/config/mutable/sanitize_allowlist.txt
-  shed_data_manager_config_file: /galaxy/server/config/mutable/shed_data_manager_conf.xml
-  shed_tool_config_file: /galaxy/server/config/mutable/editable_shed_tool_conf.xml
-  shed_tool_data_table_config: /galaxy/server/config/mutable/shed_tool_data_table_conf.xml
-  tool_data_path: '/galaxy/server/database/tool-data'
-  tool_dependency_dir: '/galaxy/server/database/deps'
-  tool_path: '/galaxy/server/database/tools'
-  
\ No newline at end of file
diff --git a/config/job_conf.yml.k8s_interactivetools b/config/job_conf.yml.k8s_interactivetools
deleted file mode 100644
index 4f33951cac8..00000000000
--- a/config/job_conf.yml.k8s_interactivetools
+++ /dev/null
@@ -1,41 +0,0 @@
-execution:
-  default: dynamic_k8s_dispatcher
-  environments:
-    dynamic_k8s_dispatcher:
-      docker_default_container_id: 'galaxy/galaxy-min:latest'
-      container_monitor: false
-      docker_enabled: true
-      function: k8s_container_mapper
-      container_monitor: false
-      runner: dynamic
-      type: python
-    local:
-      runner: local
-handling:
-  assign:
-  - db-skip-locked
-limits:
-- type: registered_user_concurrent_jobs
-  value: 5
-- type: anonymous_user_concurrent_jobs
-  value: 2
-runners:
-  k8s:
-    k8s_cleanup_job: onsuccess
-    k8s_fs_group_id: "101"
-    k8s_galaxy_instance_id: 'my-galaxy-instance'
-    k8s_namespace: 'galaxy-namespace'
-    k8s_pod_priority_class: 'my-galaxy-instance-job-priority'
-    k8s_pull_policy: IfNotPresent
-    k8s_supplemental_group_id: "101"
-    k8s_use_service_account: true
-    k8s_run_as_user_id: "0"
-    k8s_run_as_group_id: "0"
-    k8s_interactivetools_use_ssl: true
-    k8s_interactivetools_ingress_annotations:
-      cert-manager.io/cluster-issuer: letsencrypt-prod
-      kubernetes.io/tls-acme: "true"
-    load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
-  local:
-    load: galaxy.jobs.runners.local:LocalJobRunner
-    workers: 4
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index e50748de254..0a344004129 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -314,6 +314,15 @@
                  a requirement of the other.
 
                  -->
+            <!-- <param id="k8s_run_as_user_id">101</param> -->
+            <!-- ID of user that should be used by the tool command in the job containers -->
+            <!-- <param id="k8s_run_as_group_id">101</param> -->
+            <!-- ID of group that should be used by the tool command in the job containers -->
+            <!-- <param id="k8s_interactivetools_use_ssl">True</param> -->
+            <!-- Whether to enabled HTTPS access in the k8s ingress spec generated for each interactive tools -->
+            <!-- <param id="k8s_interactivetools_ingress_annotations">{'cert-manager.io/cluster-issuer': 'letsencrypt-prod'}</param> -->
+            <!-- Annotations to add to the metadata section in the k8s ingress generated for each interactive tools -->
+
         </plugin>
         <plugin id="godocker" type="runner" load="galaxy.jobs.runners.godocker:GodockerJobRunner">
             <!-- Go-Docker is a batch computing/cluster management tool using Docker
@@ -1021,6 +1030,11 @@
             <!-- REQUIRED: To play nicely with the existing galaxy setup for containers. This could be set though
                  internally by the runner. -->
             <param id="docker_enabled">true</param>
+            <param id="container_monitor">true</param>
+            <!-- Flag for appending the container monitor command to jobs. This should be set to false
+                 when running Interactive Tools with the kubernetes runner, but is needed for running with the
+                 local docker runner.
+            -->
         </destination>
         <destination id="kubernetes" runner="k8s">
             <!-- <param id="requests_cpu">500m</param> -->