Add GALAXY_LOG_DIR to exports for galaxy, change skip_machine_users t…

…o a skippable tag
usegalaxy-au · Jan 16, 2025 · bbb00b7 · bbb00b7
1 parent 0d88719
commit bbb00b7
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Showing 4 changed files with 11 additions and 3 deletions.
diff --git a/group_vars/galaxyservers.yml b/group_vars/galaxyservers.yml
@@ -118,6 +118,7 @@ galaxy_mutable_config_dir: "{{ galaxy_root }}/var"
 galaxy_mutable_data_dir: "{{ galaxy_root }}"
 galaxy_config_dir: "{{ galaxy_root }}/config"
 galaxy_job_working_directory: "{{ galaxy_tmp_dir }}/job_working_directory"
+galaxy_pulsar_app_config_file: "{{ galaxy_config_dir }}/pulsar_app.yml"
 galaxy_conda_prefix: "{{ galaxy_tools_indices_dir }}/tool_dependencies/_conda"
 galaxy_conda_exec: mamba
 
@@ -402,6 +403,7 @@ lsyncd_source: /mnt/galaxy
 lsyncd_target: /mnt/ghost-galaxy-app
 lsyncd_exclude:
   - cache
+  - log
 lsyncd_max_user_watches: 524288
 
 # debugging settings

diff --git a/roles/common/tasks/bashrc.yml b/roles/common/tasks/bashrc.yml
@@ -28,12 +28,16 @@
         export GALAXY_ROOT={{ galaxy_server_dir }}
         export GALAXY_CONFIG_FILE={{ galaxy_config_file }}
         export GALAXY_JWD_PATH="{{ galaxy_job_working_directory }}"
+        export GALAXY_LOG_DIR="{{ galaxy_log_dir }}"
+        export GALAXY_PULSAR_APP_CONF="{{ galaxy_pulsar_app_config_file }}"
         {% endif %}
 - name: Template common_bashrc path
   copy:
     dest: "{{ common_bashrc_functions_file }}"
     mode: 0755
     content: |
+        # Common variables and functions for ubuntu and human users
+
         {% if is_galaxy_head_node %}
         # galaxy
         jwd() { # print path of job working directory for job id

diff --git a/roles/common/tasks/main.yml b/roles/common/tasks/main.yml
@@ -83,11 +83,13 @@
 
 - name: Add machine users
   import_tasks: machine_users.yml
-  when: not skip_machine_users|d(False)
+  tags:
+    - users
 
 - name: Add variables to bashrc files
   import_tasks: bashrc.yml
-  when: not skip_machine_users|d(False)
+  tags:
+    - users
 
 - name: Add extra ssh keys
   include_tasks: extra_keys.yml

diff --git a/roles/common/templates/bashrc/get_jwd_path_galaxy.py.j2 b/roles/common/templates/bashrc/get_jwd_path_galaxy.py.j2
@@ -23,4 +23,4 @@ def get_jwd_path(job_id, prefix):
 
 
 if __name__ == '__main__':
-    main()
+    main()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -23,4 +23,4 @@ def get_jwd_path(job_id, prefix):


		if __name__ == '__main__':
		main()
		main()