Rename variable and corresponding file shed_tool_list_file to tool_li…

…st_file

README.md

@@ -21,7 +21,7 @@ Role variables
 ### Optional variables ###
 - `galaxy_instance_url`: (default `127.0.0.1:8080`) a URL or an IP address for
   the Galaxy instance where the tools are to be installed
-- `shed_tool_list_file`: (default `files/tool_list.yaml`) the file
+- `tool_list_file`: (default `files/tool_list.yaml`) the file
   containing all the tools to be installed
 - `base_dir`: (default: `/tmp`) the system path from where this role will be run
 

defaults/main.yml

@@ -3,5 +3,5 @@
 galaxy_install_tools: yes
 
 galaxy_instance_url: 127.0.0.1:8080
-shed_tool_list_file: tool_list.yaml
+tool_list_file: tool_list.yaml
 base_dir: /tmp

files/README.md

@@ -27,7 +27,6 @@ exoerimental implementation and you are likely to experience many issues.
 
     python install_tool_shed_tools.py -d <dbkey list file>
 
-
 [ts]: http://genomebiology.com/2014/15/2/403
 [bb]: http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.toolshed
 [dm]: https://wiki.galaxyproject.org/Admin/Tools/DataManagers

files/install_tool_shed_tools.py

@@ -3,7 +3,7 @@
 into an instance of Galaxy.
 
 Galaxy instance details and the installed tools need to be provided in YAML
-format in a separate file; see ``shed_tool_list.yaml.sample`` for a sample of
+format in a separate file; see ``tool_list.yaml.sample`` for a sample of
 such file.
 
 When installing tools, this script expects any `tool_panel_section_id` provided
@@ -80,7 +80,7 @@ def _setup_global_logger():
     return logger
 
 
-def load_input_file(tool_list_file='tool_shed_tool_list.yaml'):
+def load_input_file(tool_list_file='tool_list.yaml'):
     """
     Load YAML from the `tool_list_file` and return a dict with the content.
     """
@@ -264,7 +264,7 @@ def _parse_cli_options():
     parser.add_option("-t", "--toolsfile",
                       dest="tool_list_file",
                       default=None,
-                      help="Tools file to use (see shed_tool_list.yaml.sample)",)
+                      help="Tools file to use (see tool_list.yaml.sample)",)
     parser.add_option("-d", "--dbkeysfile",
                       dest="dbkeys_list_file",
                       default=None,

tasks/tools.yml

@@ -10,14 +10,14 @@
   copy: src=install_tool_shed_tools.py dest={{ base_dir }}/install_tool_shed_tools.py
 
 - name: Copy tool list file
-  copy: src={{ shed_tool_list_file }} dest={{ base_dir }}/shed_tool_list.yaml
+  copy: src={{ tool_list_file }} dest={{ base_dir }}/tool_list.yaml
 
 - name: Install Tool Shed tools
-  command: chdir={{ base_dir }} {{ base_dir }}/venv/bin/python install_tool_shed_tools.py -t shed_tool_list.yaml -a {{ api_key }} -g {{ galaxy_instance_url }}
+  command: chdir={{ base_dir }} {{ base_dir }}/venv/bin/python install_tool_shed_tools.py -t tool_list.yaml -a {{ api_key }} -g {{ galaxy_instance_url }}
   ignore_errors: true
 
 - name: Remove tool management scripts/file
   file: dest={{ base_dir }}/{{ item }} state=absent
   with_items:
     - install_tool_shed_tools.py
-    - shed_tool_list.yaml
+    - tool_list.yaml