diff --git a/group_vars/all b/group_vars/all index 857178ac..77fadd3b 100644 --- a/group_vars/all +++ b/group_vars/all @@ -199,6 +199,7 @@ igv_modulefiles_dir: "{{ cluster_shared_folder }}/modulefiles/{{ igv_module_name }}" igv_ood_app_dir: "{{ ood_sys_apps_dir }}/{{ igv_module_name }}" igv_ood_repo: "https://github.com/uabrc/ood_igv.git" + igv_ood_app_version: "v1" igv_versions: - "2.12.2-Java-11" diff --git a/roles/ood_igv/files/script.sh.erb b/roles/ood_igv/files/script.sh.erb deleted file mode 100644 index 3d1c1e5a..00000000 --- a/roles/ood_igv/files/script.sh.erb +++ /dev/null @@ -1,37 +0,0 @@ -#!/usr/bin/env bash - - -# Clean the environment -module reset - -# Set working directory to home directory -cd "${HOME}" - -# -# Launch Xfce Window Manager and Panel -# - -( - export SEND_256_COLORS_TO_REMOTE=1 - export XDG_CONFIG_HOME="<%= session.staged_root.join("config") %>" - export XDG_DATA_HOME="<%= session.staged_root.join("share") %>" - export XDG_CACHE_HOME="$(mktemp -d)" - module restore - set -x - xfwm4 --compositor=off --daemon --sm-client-disable - xsetroot -solid "#D3D3D3" - xfsettingsd --sm-client-disable - xfce4-panel --sm-client-disable -) & - -# -# Start Integrative Genomics Viewer -# - -# Load the required environment -module load <%= context.version %> -# Launch IGV -module list -set -x -igvtools_gui.command & -igv.sh diff --git a/roles/ood_igv/tasks/main.yaml b/roles/ood_igv/tasks/main.yaml index d4342a28..2e41812a 100644 --- a/roles/ood_igv/tasks/main.yaml +++ b/roles/ood_igv/tasks/main.yaml @@ -12,19 +12,4 @@ repo: "{{ igv_ood_repo }}" dest: "{{ igv_ood_app_dir }}" clone: yes - -- name: Replace form.yml - template: - src: form.yml.j2 - dest: "{{ igv_ood_app_dir }}/form.yml" - -- name: Replace form submission template - template: - src: submit.yml.erb.j2 - dest: "{{ igv_ood_app_dir }}/submit.yml.erb" - -- name: Replace form script template - copy: - src: script.sh.erb - dest: "{{ igv_ood_app_dir }}/template/script.sh.erb" - mode: '0755' + version: "{{ igv_ood_app_version }}" diff --git a/roles/ood_igv/templates/form.yml.j2 b/roles/ood_igv/templates/form.yml.j2 deleted file mode 100644 index 5452676d..00000000 --- a/roles/ood_igv/templates/form.yml.j2 +++ /dev/null @@ -1,52 +0,0 @@ ---- -cluster: "{{ cluster_name }}" -attributes: - bc_num_hours: - value: 1 - - bc_num_slots: - label: Number of CPU - value: 1 - min: 1 - max: 24 - step: 1 - - bc_num_mems: - widget: "number_field" - label: Memory per CPU (GB) - value: 4 - min: 1 - max: 128 - step: 1 - - bc_partition: - widget: select - label: Partition - options: - - [ "express", "express" ] - - [ "short", "short" ] - - [ "medium", "medium" ] - - [ "long", "long" ] - - [ "interactive", "interactive" ] - - [ "pascalnodes", "pascalnodes" ] - - [ "pascalnodes-medium", "pascalnodes-medium" ] - - [ "largemem", "largemem" ] - - [ "largemem-long", "largemem-long" ] - - [ "amd-hdr100", "amd-hdr100" ] - - version: - widget: select - label: "IGV version" - help: "This defines the version of IGV you want to load." - options: -{% for ver in igv_versions %} - - [ "{{ ver }}", "{{ igv_module_name }}/{{ ver }}" ] -{% endfor %} - -form: - - version - - bc_num_hours - - bc_partition - - bc_num_slots - - bc_num_mems - - bc_email_on_started diff --git a/roles/ood_igv/templates/submit.yml.erb.j2 b/roles/ood_igv/templates/submit.yml.erb.j2 deleted file mode 100644 index d32e9497..00000000 --- a/roles/ood_igv/templates/submit.yml.erb.j2 +++ /dev/null @@ -1,14 +0,0 @@ ---- -batch_connect: - template: "vnc" -script: - native: - - "-N 1" - - "-n <%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>" - - "--mem-per-cpu=<%= bc_num_mems.blank? ? 4 : bc_num_mems.to_i %>G" - - "--partition=<%= bc_partition %>" - - "--time=<%= bc_num_hours.blank? ? 1 : bc_num_hours.to_i %>:00:00" - - "--job-name=ood-{{ igv_module_name|lower }}" -<%- if bc_partition.include? "pascalnodes" -%> - - "--gres=gpu:1" -<%- end -%>