Galaxy configuration for TESP

files/galaxy-qa2.galaxy.cloud.e-infra.cz/tool_list.yaml

@@ -1,20 +1,19 @@
 tools:
-- name: iedb_api
-  owner: iuc
+- name: fastqc
+  owner: devteam
   revisions:
-  - 7ed6dda64a81
-  tool_panel_section_label: Get Data
+  - 5ec9f6bceaee
+  tool_panel_section_label: FASTA/FASTQ
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: dbbuilder
-  owner: galaxyp
+- name: bwa
+  owner: devteam
   revisions:
-  - 983bf725dfc2
-  tool_panel_section_label: Get Data
+  - 2477830927ec
+  tool_panel_section_label: Mapping
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: sra_tools
-  owner: iuc
+- name: alphafold2
+  owner: galaxy-australia
   revisions:
-  - 734abc7ac21d
-  - f5ea3ce9b9b0
-  tool_panel_section_label: Get Data
-  tool_shed_url: toolshed.g2.bx.psu.edu
+  - 3f188450ca4f
+  tool_panel_section_label: ChemicalToolBox
+  tool_shed_url: toolshed.g2.bx.psu.edu

group_vars/galaxyservers.yml

@@ -46,10 +46,12 @@ galaxy_job_config:
       amqp_publish_retry: true
       amqp_publish_retry_max_retries: 60
       manager: _default_
+    tes_runner:
+      load: galaxy.jobs.runners.tes:TESJobRunner
   handling:
     assign: ['db-skip-locked']
   execution:
-    default: tpv_dispatcher
+    default: tesp_env
     environments:
       local_env:
         runner: local_runner
@@ -63,6 +65,10 @@ galaxy_job_config:
           - https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml
           - "{{ tpv_config_dir }}/tpv_rules_meta.yml"
           - "{{ tpv_config_dir }}/tpv_rules_{{ inventory_hostname }}.yml"
+      tesp_env:
+        runner: tes_runner
+        tes_master_addr: http://147.251.255.46:8080
+        default_docker_image: hub.cerit.io/josef_handl/tesp-test-image
   resources:
     default: default
     groups:

host_vars/galaxy-qa2.galaxy.cloud.e-infra.cz/vars.yml

@@ -1,5 +1,5 @@
 galaxy_build_client: false
-galaxy_commit_id: release_24.2
+galaxy_commit_id: latest
 
 csnt_brand: QA2-TEST
 # csnt_enable_account_interface: false
@@ -31,3 +31,5 @@ galaxy_config_files:
     dest: "{{ galaxy_config.galaxy.tool_config_file[0] }}"
   - src: files/galaxy/config/oidc_config.xml
     dest: "{{ galaxy_config_dir }}/oidc_config.xml"
+
+galaxy_repo: "https://github.com/BorisYourich/galaxy.git"

roles/galaxyproject.galaxy/defaults/main.yml

@@ -206,7 +206,7 @@ galaxy_tmpclean_command: "{{ _galaxy_tmpclean_command[(ansible_os_family | lower
 #galaxy_node_version: "XX.YY.Z"
 
 # Where to clone Galaxy from. Backwards compatibility with galaxy_git_repo
-galaxy_repo: "{{ galaxy_git_repo | default('https://github.com/galaxyproject/galaxy.git') }}"
+# galaxy_repo: "{{ galaxy_git_repo | default('https://github.com/galaxyproject/galaxy.git') }}"
 
 # Automatically delete things in the repo that do not belong there
 galaxy_force_checkout: no
@@ -220,7 +220,6 @@ galaxy_commit_id: "{{ galaxy_changeset_id | default('master') }}"
 
 # Download URL (if used)
 galaxy_download_url: "{{ galaxy_repo | replace('.git', '') }}/archive/{{ galaxy_commit_id }}.tar.gz"
-
 #
 # Path and Galaxy configuration
 #