Merge pull request #56 from galaxyproject/usegalaxy-privileged-extras

Support for installing local tools and dynamic job rules from the playbook

README.md

@@ -138,6 +138,15 @@ Options for configuring Galaxy and controlling which version is installed.
   file. See the Example Playbooks below for usage.
 - `galaxy_config_files`: List of hashes (with `src` and `dest` keys) of files to copy from the control machine.
 - `galaxy_config_templates`: List of hashes (with `src` and `dest` keys) of templates to fill from the control machine.
+- `galaxy_local_tools`: List of local tool files or directories to copy from the control machine, relative to
+  `galaxy_local_tools_src_dir` (default: `files/galaxy/tools` in the playbook).
+- `galaxy_local_tools_dir`: Directory on the Galaxy server where local tools will be installed.
+- `galaxy_dynamic_job_rules`: List of dynamic job rules to copy from the control machine, relative to
+  `galaxy_dynamic_job_rules_src_dir` (default: `files/galaxy/dynamic_job_rules` in the playbook).
+- `galaxy_dynamic_job_rules_dir` (default: `{{ galaxy_server_dir }}/lib/galaxy/jobs/rules`): Directory on the Galaxy
+  server where dynamic job rules will be installed. If changed from the default, ensure the directory is on Galaxy's
+  `$PYTHONPATH` (e.g. in `{{ galaxy_venv_dir }}/lib/python2.7/site-packages`) and configure the dynamic rules plugin in
+  `job_conf.xml` accordingly.
 - `galaxy_repo` (default: `https://github.com/galaxyproject/galaxy.git`): Upstream Git repository from which Galaxy
   should be cloned.
 - `galaxy_commit_id` (default: `master`): A commit id, tag, branch, or other valid Git reference that Galaxy should be
@@ -311,4 +320,4 @@ This role was written and contributed to by the following people:
 - [Simon Belluzzo](https://github.com/simonalpha)
 - [John Chilton](https://github.com/jmchilton)
 - [Nate Coraor](https://github.com/natefoo)
-- [Helena Rasche](https://github.com/erasche)
+- [Helena Rasche](https://github.com/erasche)

defaults/main.yml

@@ -97,6 +97,19 @@ galaxy_privsep_dirs:
   - "{{ galaxy_venv_dir }}"
   - "{{ galaxy_server_dir }}"
   - "{{ galaxy_config_dir }}"
+  - "{{ galaxy_local_tools_dir }}"
+
+# Local (relative to playbook) path to local tools
+galaxy_local_tools_src_dir: files/galaxy/tools
+
+# Local (relative to playbook) path to dynamic job rules
+galaxy_dynamic_job_rules_src_dir: files/galaxy/dynamic_job_rules
+
+# Remote path to dynamic job rules (must be on Galaxy's $PYTHONPATH if not the default)
+galaxy_dynamic_job_rules_dir: "{{ galaxy_server_dir }}/lib/galaxy/jobs/rules"
+
+# List of dynamic rules to install
+galaxy_dynamic_job_rules: []
 
 #
 # Version control
@@ -125,6 +138,11 @@ galaxy_download_url: "{{ galaxy_repo | replace('.git', '') }}/archive/{{ galaxy_
 # Directory layout for deployment (legacy is the default)
 #galaxy_layout: legacy
 
+# List of tool configs to load
+galaxy_tool_config_files:
+  - "{{ galaxy_server_dir }}/config/tool_conf.xml.sample"
+  - "{{ galaxy_shed_tool_conf_file }}"
+
 # The shed tool conf path is needed separate from the value of tool_conf for instantiation
 galaxy_shed_tool_conf_file: "{{ galaxy_mutable_config_dir }}/shed_tool_conf.xml"
 
@@ -176,7 +194,7 @@ galaxy_app_config_default:
   tool_dependency_dir: "{{ galaxy_tool_dependency_dir }}"
 
   # Static config files
-  tool_config_file: "{{ galaxy_server_dir }}/config/tool_conf.xml.sample,{{ galaxy_shed_tool_conf_file }}"
+  tool_config_file: "{{ galaxy_tool_config_files | join(',') }}"
 
   # Everything else
   visualization_plugins_directory: "config/plugins/visualizations"

tasks/layout.yml

@@ -16,6 +16,7 @@
     - galaxy_mutable_config_dir
     - galaxy_shed_tools_dir
     - galaxy_cache_dir
+    - galaxy_local_tools_dir
 
 - name: Check that any explicitly set Galaxy config options match the values of explicitly set variables
   assert:

tasks/static_setup.yml

@@ -26,6 +26,47 @@
         backup: "{{ galaxy_backup_configfiles }}"
       with_items: "{{ galaxy_config_templates }}"
 
+    - name: Install local tools
+      copy:
+        src: "{{ galaxy_local_tools_src_dir }}/{{ item }}"
+        dest: "{{ galaxy_local_tools_dir }}/{{ item }}"
+      with_items: "{{ galaxy_local_tools | default([]) }}"
+      when: galaxy_local_tools is defined
+
+    - name: Install local_tool_conf.xml
+      template:
+        src: local_tool_conf.xml.j2
+        dest: "{{ galaxy_config_dir }}/local_tool_conf.xml"
+      when: galaxy_local_tools is defined
+
+    - name: Append local_tool_conf.xml to tool_config_file Galaxy config option
+      set_fact:
+        galaxy_tool_config_files: "{{ galaxy_tool_config_files }} + ['{{ galaxy_config_dir ~ '/local_tool_conf.xml' }}']"
+      when: galaxy_local_tools is defined
+
+    - name: Ensure dynamic job rules paths exists
+      file:
+        path: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}"
+        state: directory
+      loop_control:
+        label: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}"
+      with_items: "{{ galaxy_dynamic_job_rules }}"
+
+    - name: Install dynamic job rules
+      copy:
+        src: "{{ galaxy_dynamic_job_rules_src_dir }}/{{ item }}"
+        dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item }}"
+      with_items: "{{ galaxy_dynamic_job_rules }}"
+
+    - name: Ensure dynamic rule __init__.py's exist
+      copy:
+        content: ""
+        dest: "{{ galaxy_dynamic_job_rules_dir }}/{{ item | dirname }}/__init__.py"
+        force: no
+      loop_control:
+        label: "{{ galaxy_dynamic_job_rules_dir }}/{{ ((item | dirname) != '') | ternary ((item | dirname) ~ '/', '') }}__init__.py"
+      with_items: "{{ galaxy_dynamic_job_rules }}"
+
     - name: Create Galaxy configuration file
       template:
         src: "{{ galaxy_config_file_template }}"

templates/local_tool_conf.xml.j2

@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='utf-8'?>
+<toolbox monitor="true" tool_path="{{ galaxy_local_tools_dir }}">
+{% for tool in galaxy_local_tools %}
+{% if tool.endswith('.xml') %}
+    <tool file="{{ tool }}" />
+{% endif %}
+{% endfor %}
+</toolbox>

vars/layout-custom.yml

@@ -9,6 +9,7 @@
 # Layout defaults
 __galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
 __galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_local_tools_dir: null
 __galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options

vars/layout-legacy-improved.yml

@@ -6,6 +6,7 @@ __galaxy_config_dir: "{{ galaxy_server_dir }}/config"
 __galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
 __galaxy_mutable_config_dir: "{{ galaxy_server_dir }}/config"
 __galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}"
+__galaxy_local_tools_dir: null
 __galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options

vars/layout-legacy.yml

@@ -6,6 +6,7 @@ __galaxy_config_dir: "{{ galaxy_server_dir }}"
 __galaxy_mutable_data_dir: "{{ galaxy_server_dir }}/database"
 __galaxy_mutable_config_dir: "{{ galaxy_server_dir }}"
 __galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}"
+__galaxy_local_tools_dir: null
 __galaxy_shed_tools_dir: "{{ galaxy_server_dir }}/../shed_tools"
 
 # These correspond to galaxy config options

vars/layout-opt.yml

@@ -1,12 +1,13 @@
 ---
 
 # Layout defaults
-__galaxy_server_dir: "/opt/galaxy/server"
-__galaxy_venv_dir: "/opt/galaxy/venv"
+__galaxy_server_dir: "/opt/galaxy"
+__galaxy_venv_dir: "/var/opt/galaxy/venv"
 __galaxy_config_dir: "/etc/opt/galaxy"
-__galaxy_mutable_data_dir: "/var/opt/galaxy"
+__galaxy_mutable_data_dir: "/var/opt/galaxy/data"
 __galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
 __galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_local_tools_dir: "/var/opt/galaxy/local_tools"
 __galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options

vars/layout-root-dir.yml

@@ -7,6 +7,7 @@ __galaxy_config_dir: "{{ galaxy_root }}/config"
 __galaxy_mutable_data_dir: "{{ galaxy_root }}/var"
 __galaxy_mutable_config_dir: "{{ galaxy_mutable_data_dir }}/config"
 __galaxy_cache_dir: "{{ galaxy_mutable_data_dir }}/cache"
+__galaxy_local_tools_dir: "{{ galaxy_root }}/local_tools"
 __galaxy_shed_tools_dir: "{{ galaxy_mutable_data_dir }}/shed_tools"
 
 # These correspond to galaxy config options