diff README.md @ 1:1aeef205e648 draft

planemo upload
author mingchen0919
date Sun, 01 Apr 2018 16:48:53 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Sun Apr 01 16:48:53 2018 -0400
@@ -0,0 +1,63 @@
+# Elastic Galaxy Tools
+
+* [What are Elastic Galaxy Tools](#what-are-elastic-galaxy-tools?)
+* [How to use Elastic Galaxy Tools](#how-to-use-elastic-galaxy-tools?)
+* [How to develop an Elastic Galaxy Tool](#how-to-develop-an-elastic-galaxy-tool?)
+    + [Publish a Galaxy Tool](#publish-a-galaxy-tool)
+
+
+
+
+## What are Elastic Galaxy Tools?
+
+**Elastic Galaxy tools** is a type of Galaxy tools that have elastic user interfaces. Users can adjust the
+number of input fields a tool can have, just like using a command line tool. When using a command line tool,
+users can choose which (non-required) options to use. I hope Galaxy users can do the same thing, but without
+actually writing any command line scripts.
+ 
+
+## How to use Elastic Galaxy Tools?
+
+Although any (Elastic) Galaxy tool is a wrapper of a command line tool which enables performing data analysis
+through web interfaces without actually writing any command line script, understanding how to read command line
+manuals will help you use Elastic Galaxy tools. 
+
+Running a command line tool is very simple. You start with the tool name, then you specify options (also called flags) 
+that the tool can recognize. The tool manual should tell you which options the tool can recognize. An option may or may 
+not have a value followed. Some options are required and some are optional. You have to use all required options to 
+successfully run a command line tool. However, you can use as many optional options as you want in a call of a command 
+line tool.
+
+## How to develop an Elastic Galaxy Tool?
+
+### Publish a Galaxy tool
+
+We can use the tool **planemo** to easily publish our Galaxy tools to Tool Shed or test Tool Shed. 
+More details can be found **[here](http://planemo.readthedocs.io/en/latest/publishing.html)**.
+
+* Publish to test Tool Shed
+
+```bash
+planemo shed_create --shed_target testtoolshed
+``` 
+
+* Update tool repository in test Tool Shed
+
+```bash
+planemo shed_update --check_diff --shed_target testtoolshed
+```
+
+* Publish to Tool Shed
+
+```bash
+planemo shed_create --shed_target toolshed
+```
+
+* Update tool repository in Tool Shed
+
+```bash
+planemo shed_update --check_diff --shed_target toolshed
+```
+
+
+