From 6dc802a94175e7653a8f5a162e4afc57db1b0dd7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 3 May 2017 09:45:38 -0400 Subject: [PATCH 1/2] Rev galaxy-extras for munge fix in galaxyproject/ansible-galaxy-extras#133. --- roles/galaxyprojectdotorg.galaxy-extras | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/roles/galaxyprojectdotorg.galaxy-extras b/roles/galaxyprojectdotorg.galaxy-extras index 0f7a0b8..78a4509 160000 --- a/roles/galaxyprojectdotorg.galaxy-extras +++ b/roles/galaxyprojectdotorg.galaxy-extras @@ -1 +1 @@ -Subproject commit 0f7a0b899d68ce36a40778745d1ffe9a5137149a +Subproject commit 78a4509c77ae4e25417cdcb49f7827f328b8c3cb From b5eb4d6345c3d9eaaa3092be2468b0f8caa11673 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 3 May 2017 08:28:20 -0400 Subject: [PATCH 2/2] Devbox VM Updates - Disable scrollback on output (per #85). - Increase lines of scrollback (per #85). - Increase font size in terminal (per #85). - Disable screensaver (per #85). - Update to latest Ubuntu server 16.04 ISO. - Update bash hacking to add Minicond3 instead of Miniconda2 to the path - use planemo to fetch it. - Add symbolic links to Galaxy logs to the Desktop. - Cleanup some codebox junk that wasn't deleted properly previously. --- .../defaults/main.yml | 8 ++--- .../galaxyprojectdotorg.devbox/tasks/main.yml | 32 +++++++++++++++---- .../templates/supervisor.conf.j2 | 7 ---- .../templates/terminalrc.j2 | 29 +++++++++++++++++ 4 files changed, 57 insertions(+), 19 deletions(-) delete mode 100644 roles/galaxyprojectdotorg.devbox/templates/supervisor.conf.j2 create mode 100644 roles/galaxyprojectdotorg.devbox/templates/terminalrc.j2 diff --git a/roles/galaxyprojectdotorg.devbox/defaults/main.yml b/roles/galaxyprojectdotorg.devbox/defaults/main.yml index eecddc0..faaeb96 100644 --- a/roles/galaxyprojectdotorg.devbox/defaults/main.yml +++ b/roles/galaxyprojectdotorg.devbox/defaults/main.yml @@ -1,8 +1,6 @@ -codebox_path: "/opt/galaxy/codebox" -codebox_port: 8991 - -codebox_version: 0.8.3 - small_tool_conf: no galaxy_devbox_include_x: false + +galaxy_devbox_terminal_font: "DejaVu Sans Mono" +galaxy_devbox_terminal_font_size: 14 diff --git a/roles/galaxyprojectdotorg.devbox/tasks/main.yml b/roles/galaxyprojectdotorg.devbox/tasks/main.yml index 44b899f..55bfefc 100644 --- a/roles/galaxyprojectdotorg.devbox/tasks/main.yml +++ b/roles/galaxyprojectdotorg.devbox/tasks/main.yml @@ -53,6 +53,10 @@ - firefox when: galaxy_devbox_include_x +- name: Remove light-locker to disable screen locking in VM. + apt: name=light-locker state=absent update_cache=yes + when: galaxy_devbox_include_x + - name: Add Google key for Chrome installation apt_key: url: https://dl.google.com/linux/linux_signing_key.pub @@ -149,6 +153,14 @@ file: src={{ dev_tool_conf_dir }} dest={{ dev_user_home }}/Desktop/tools state=link owner={{ dev_user_name }} group={{ dev_user_group }} force=true when: galaxy_devbox_include_x +- name: Configure Desktop link to Galaxy web log. + file: src={{ uwsgi_log if galaxy_uwsgi else galaxy_log_dir + "/galaxy_web0.log" }} dest="{{ dev_user_home }}/Desktop/Galaxy Web Process.log" state=link owner={{ dev_user_name }} group={{ dev_user_group }} force=true + when: galaxy_devbox_include_x + +- name: Configure Desktop link to Galaxy handler log. + file: src={{ galaxy_log_dir }}/handler0.log dest="{{ dev_user_home }}/Desktop/Galaxy Job Handler.log" state=link owner={{ dev_user_name }} group={{ dev_user_group }} force=true + when: galaxy_devbox_include_x + - name: Install the dev tools apt: name={{ item }} state=latest update_cache=yes with_items: @@ -217,20 +229,26 @@ - name: Ensure existence of target directory for next step. file: path={{ dev_user_home }}/.config/xfce4/xfconf/xfce-perchannel-xml state=directory owner={{ dev_user_name }} group={{ dev_user_group }} -- name: Download miniconda +- name: "Add the keyboard layout switcher to the panel." + template: src=xfce4-panel.xml.j2 dest={{ dev_user_home }}/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml become: True become_user: "{{ dev_user_name }}" - shell: "cd {{ dev_user_home }} && curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh && bash miniconda.sh -b" - -- name: Add miniconda bin to PATH. - lineinfile: "dest={{ dev_user_shellrc }} line='export PATH=$PATH:{{ dev_user_home }}/miniconda2/bin/'" + when: galaxy_devbox_include_x -- name: "Add the keyboard layout switcher to the panel." - template: src=xfce4-panel.xml.j2 dest={{ dev_user_home }}/.config/xfce4/xfconf/xfce-perchannel-xml/xfce4-panel.xml +- name: "Add a xfce4-terminal configuration for this VM" + template: src=xfce4-panel.xml.j2 dest={{ dev_user_home }}/.config/xfce4/terminal/terminalrc become: True become_user: "{{ dev_user_name }}" when: galaxy_devbox_include_x +- name: Download and install Miniconda 3 + become: True + become_user: "{{ dev_user_name }}" + shell: "{{ dev_planemo_virtualenv }}/bin/planemo conda_init" + +- name: Add Miniconda 3 bin to PATH. + lineinfile: "dest={{ dev_user_shellrc }} line='export PATH=$PATH:{{ dev_user_home }}/miniconda3/bin/'" + - name: "Add test script to check machine." template: src=check-planemo-machine.sh.j2 dest=/usr/bin/check-planemo-machine.sh mode=0755 become: True diff --git a/roles/galaxyprojectdotorg.devbox/templates/supervisor.conf.j2 b/roles/galaxyprojectdotorg.devbox/templates/supervisor.conf.j2 deleted file mode 100644 index e34c820..0000000 --- a/roles/galaxyprojectdotorg.devbox/templates/supervisor.conf.j2 +++ /dev/null @@ -1,7 +0,0 @@ -[program:codebox] -directory = {{ codebox_path }} -command = /bin/bash -c 'export HOME=/home/{{ galaxy_user_name }}; export PORT={{ codebox_port }}; export WORKSPACE_DIR={{ dev_tool_conf_dir }}; node {{ codebox_path }}/node_modules/codebox/bin/codebox.js run' -autostart = true -autorestart = true -user = {{ galaxy_user_name }} -redirect_stderr = true diff --git a/roles/galaxyprojectdotorg.devbox/templates/terminalrc.j2 b/roles/galaxyprojectdotorg.devbox/templates/terminalrc.j2 new file mode 100644 index 0000000..8cfcb4a --- /dev/null +++ b/roles/galaxyprojectdotorg.devbox/templates/terminalrc.j2 @@ -0,0 +1,29 @@ +[Configuration] +ColorForeground=#b7b7b7 +ColorBackground=#131926 +ColorCursor=#0f4999 +ColorSelection=#163b59 +ColorSelectionUseDefault=FALSE +ColorBoldUseDefault=FALSE +ColorPalette=#000000;#aa0000;#44aa44;#aa5500;#0039aa;#aa22aa;#1a92aa;#aaaaaa;#777777;#ff8787;#4ce64c;#ded82c;#295fcc;#cc58cc;#4ccce6;#ffffff +FontName={{ galaxy_devbox_terminal_font }} {{ galaxy_devbox_terminal_font_size }} +MiscAlwaysShowTabs=FALSE +MiscBell=FALSE +MiscBordersDefault=TRUE +MiscCursorBlinks=FALSE +MiscCursorShape=TERMINAL_CURSOR_SHAPE_BLOCK +MiscDefaultGeometry=80x24 +MiscInheritGeometry=FALSE +MiscMenubarDefault=TRUE +MiscMouseAutohide=FALSE +MiscToolbarDefault=FALSE +MiscConfirmClose=TRUE +MiscCycleTabs=TRUE +MiscTabCloseButtons=TRUE +MiscTabCloseMiddleClick=TRUE +MiscTabPosition=GTK_POS_TOP +MiscHighlightUrls=TRUE +MiscScrollAlternateScreen=TRUE +TabActivityColor=#0f4999 +ScrollingLines=200000 +ScrollingOnOutput=FALSE