Merge pull request #1814 from nsoranzo/tool_shed

Cleanup Tool Shed and Tool Management slides

topics/admin/tutorials/tool-management/slides.html

@@ -240,12 +240,12 @@
 
 ---
 
-## What happens during tool installation
+## What happens when installing a tool from TS
 
-* Repository was downloaded.
-* If needed Galaxy installed the tool's dependencies using [conda][conda].
-* Galaxy created an entry for the tool in the DB.
-* Galaxy added the tool to one of the tool configs (`shed_tool_conf.xml`).
+* Repository is downloaded.
+* If needed, Galaxy installs the tool's dependencies typically using [conda][conda].
+* Galaxy creates an entry for the tool in its database.
+* Galaxy adds the tool to `shed_tool_conf.xml` .
 
 [conda]: https://conda.io/
 
@@ -269,45 +269,15 @@
 
 ---
 
-## Example config entry
-
-one entry in `integrated_tool_panel.xml`
-```xml
-<section id="filter" name="Filter and Sort" version="">
-    <tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1" />
-</section>
-```
-
----
-
-## Suites - more repos in one
-
-* To install multiple repositories some authors offer suites.
-* Suite is a single repository that 'depends' on many other.
-* If you install the suite all 'dependency repositories' will be installed too.
+## Tool panel management
 
----
-
-## Toolpanel management
-
-* How the toolpanel looks like is decided in a file called `integrated_tool_panel.xml`.
+* How the tool panel looks like is decided in a file called `integrated_tool_panel.xml`.
 * By default it resides in Galaxy's `config/` folder.
 * If missing it is generated from all other tool config files during startup.
 * Modify it if you want to reorder tools or move section.
 
----
-
-## Dependency resolvers
-
-* We aim to make Galaxy resolver-independent.
-* What resolver is going to be used for the tool dependency is determined at runtime and prioritised in `config/dependency_resolvers_conf.xml`.
-
 ```xml
-<dependency_resolvers>
-  <tool_shed_packages />
-  <galaxy_packages />
-  <conda />
-  <galaxy_packages versionless="true" />
-  <conda versionless="true" />
-</dependency_resolvers>
+<section id="filter" name="Filter and Sort" version="">
+    <tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1" />
+</section>
 ```

topics/admin/tutorials/toolshed/slides.html

@@ -9,34 +9,37 @@
 
 ---
 
-Tool Shed is to Galaxy as App Store is to iPhone.
+## Tool Shed
 
-It is a free service that hosts repositories containing Galaxy Tools.
-Installing from the Tool Shed takes care of
+- Galaxy "App Store"
+
+- It is a free service that hosts repositories containing Galaxy tools.
+
+- Installing from the Tool Shed takes care of
   - dependencies
   - reference data tables
   - configuration files
 
 ---
-Main Tool Shed (MTS) runs at http://toolshed.g2.bx.psu.edu and serves all Galaxies worldwide.
 
-Everybody can create a repository.
+## Which Tool Shed?
 
-Every repository is public including the whole history.
+The Main Tool Shed ( https://toolshed.g2.bx.psu.edu ) serves all Galaxies worldwide.
+- Everybody can create a repository.
+- Repositories are public, including their whole history.
 
 Local sheds can be run e.g. for private or custom-licensed tools.
 
 ???
 We discourage running local TS.
 
 ---
+
 ## Vocabulary
 
 * `wrapper` or `tool definition file` - The XML file that describes to Galaxy how the underlying software works, allowing Galaxy to render UI and execute the software in the right way.
---
 
 * `repository` - A versioned code archive with tool(s) in Tool Shed.
---
 
 * `revision` and `installable revision` - Every TS repo update generates a new revision but only certain (reproducibility-affecting) changes generate a new revision installable to Galaxy as a new version.
 
@@ -46,14 +49,11 @@
 ---
 ## Overview
 
-* Tool Shed is a host (not a development) platform.
---
+* The Tool Shed is a hosting (not a development) platform.
 
-* Tool Development repository should be linked from the TS repository.
---
+* Each TS repository should link to its development repository.
 
 * Tool Shed allows administrators to pick any installable revision.
---
 
 * Multiple installable revisions of any repository can be present in Galaxy.
 
@@ -64,7 +64,7 @@
 class: normal
 ## Galaxy's Configuration
 
-List of available sheds is defined in `tool_sheds_conf.xml` and Galaxy comes with the MTS enabled and the TTS disabled.
+The list of available sheds is defined in `tool_sheds_conf.xml`:
 ```xml
 <?xml version="1.0"?>
 <tool_sheds>
@@ -162,7 +162,7 @@
 ```
 
 ---
-### seqtk requirements
+### Tool requirements
 
 Requirements of the wrapper.
 ```xml
@@ -171,14 +171,15 @@
 </requirements>
 ```
 
-Galaxy is aiming to be dependency resolution agnostic.
+Galaxy aims to be dependency resolution agnostic.
 
 ---
-# Approach
+## Dependency resolution
 
 * We aim to make Galaxy resolver-independent but Conda-oriented.
 * What resolver is going to be used for the tool dependency is determined at runtime
 and prioritised in the config file `dependency_resolvers_conf.xml`.
+
 ```xml
 <dependency_resolvers>
   <tool_shed_packages />
@@ -194,31 +195,9 @@
 ```
 
 ---
-class: smaller
-### seqtk Conda package
 
-```yml
-package:
-  name: seqtk
-  version: 1.2
-source:
-  fn: v1.2.tar.gz
-  url: https://github.com/lh3/seqtk/archive/v1.2.tar.gz
-  md5: 255ffe05bf2f073dc57abcff97f11a37
-build:
-  number: 0
-requirements:
-  build:
-    - gcc   # [not osx]
-    - llvm  # [osx]
-    - zlib
-  run:
-    - zlib
-about:
-  home: https://github.com/lh3/seqtk
-  license: MIT License
-  summary: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
-test:
-  commands:
-    - seqtk seq
-```
+## Suite repositories
+
+* To install multiple repositories some authors offer suites.
+* Suite is a single repository that 'depends' on many others.
+* If you install the suite, all 'dependency repositories' will be installed too.

topics/dev/tutorials/toolshed/slides.html

@@ -697,10 +697,3 @@
 ```bash
 planemo shed_update --check_diff --shed_target local
 ```
-
----
-
-### <i class="fa fa-exclamation-circle" aria-hidden="true"></i> Key points
-
-- Use Planemo
-- Contribute to the Main Tool Shed