Fix interactive tools on the secondary HTCondor cluster

group_vars/htcondor-secondary-submit-host.yml

@@ -28,10 +28,21 @@
   [Network]
   VirtualEthernet=no
 
+nspawn_galaxy_environment_file: "{{ galaxy_user.home }}/env"
+nspawn_galaxy_environment_vars: |
+  HOME={{ galaxy_root }}
+  VIRTUAL_ENV={{ galaxy_venv_dir }}
+  PATH={{ galaxy_venv_dir }}/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
+  DOCUTILSCONFIG=''
+  PYTHONPATH={{ galaxy_server_dir }}/lib/galaxy/jobs/rules
+  {% for var in galaxy_systemd_handler_env | split %}
+  {{ var }}
+  {% endfor %}
+
 nspawn_enable: false
 nspawn_start: false
 
 nspawn_ssh: yes
 nspawn_ssh_config_path: /etc/ssh/sshd_config
 nspawn_ssh_config:
   Port: "2222"
@@ -59,9 +70,9 @@
   rsa: "[email protected] 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 /etc/ssh/ssh_host_rsa_key.pub"
 nspawn_ssh_authorized_keys:
   - "ssh-rsa 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 cloud@vgcn"
 nspawn_ssh_host_trust_container: yes
 
-nspawn_condor_systemd_run: "/usr/bin/systemd-run --uid={{ galaxy_user.uid }} --gid={{ galaxy_group.gid }} --pipe --quiet --machine {{ nspawn_name }}"
+nspawn_condor_systemd_run: "/usr/bin/systemd-run -p EnvironmentFile={{ nspawn_galaxy_environment_file }} --uid={{ galaxy_user.uid }} --gid={{ galaxy_group.gid }} --pipe --quiet --machine {{ nspawn_name }}"
 nspawn_condor_rm_command: "{{ nspawn_condor_systemd_run }} /usr/bin/condor_rm"
 nspawn_condor_ssh_to_job_command: "{{ nspawn_condor_systemd_run }} /usr/bin/condor_ssh_to_job"
 nspawn_condor_submit_command: "{{ nspawn_condor_systemd_run }} /usr/bin/condor_submit"

htcondor.yml

@@ -11,6 +11,7 @@
       changed_when: true
   vars_files:
     - mounts/mountpoints.yml
+    - secret_group_vars/all.yml
     - secret_group_vars/htcondor-secondary-submit-host.yml
   pre_tasks:
     # Because it is already disabled for sn06 and this setup is needed just
@@ -22,19 +23,19 @@
   roles:
     - kysrpex.systemd_nspawn
   post_tasks:
+    - name: Get the location of the container image.
+      ansible.builtin.shell:
+        executable: /bin/bash
+        cmd: |
+          set -o pipefail
+          machinectl image-status htcondor | grep "Path: " | awk '{$1=$1};1' | cut -d' ' -f2
+      register: nspawn_image
+      changed_when: false
+
     - name: Configure the container's sshd.
       when: nspawn_ssh and (nspawn_ssh_config is defined or nspawn_ssh_config_path is defined)
       become: true
       block:
-        - name: Get the location of the container image.
-          ansible.builtin.shell:
-            executable: /bin/bash
-            cmd: |
-              set -o pipefail
-              machinectl image-status htcondor | grep "Path: " | awk '{$1=$1};1' | cut -d' ' -f2
-          register: nspawn_image
-          changed_when: false
-
         - name: Write the sshd configuration to sshd_config.
           ansible.builtin.lineinfile:
             path: "{{ (nspawn_image.stdout, nspawn_ssh_config_path | regex_replace('(\\/*)?(.*)', '\\2')) | path_join }}"
@@ -192,6 +193,14 @@
           - "{{ nspawn_condor_ssh_to_job_command }} *"
           - "{{ nspawn_condor_submit_command }} *"
 
+    - name: Make the environment variables available to the Galaxy handlers also available to the container.
+      ansible.builtin.copy:
+        content: "{{ nspawn_galaxy_environment_vars }}"
+        dest: "{{ (nspawn_image.stdout, nspawn_galaxy_environment_file | regex_replace('(\\/*)?(.*)', '\\2')) | path_join }}"
+        owner: "{{ galaxy_user.name }}"
+        group: "{{ galaxy_group.name }}"
+        mode: "0440"
+
 - name: HTCondor cluster.
   hosts: htcondor:!sn06.galaxyproject.eu
   handlers: