From 4ea9a88fd51a5d4545fceac0fed15776b9555cc6 Mon Sep 17 00:00:00 2001
From: hdzierz <helge.dzierzon@plantandfood.co.nz>
Date: Fri, 29 Jan 2016 15:10:38 +1300
Subject: [PATCH] Added test script. Next commit will be via a pull request.

---
 README.md      |  7 +++++--
 test/README.md | 15 +++++++++++++++
 test/test.R    |  4 ++++
 test/test.Rmd  | 14 ++++++++++++++
 4 files changed, 38 insertions(+), 2 deletions(-)
 create mode 100644 test/README.md
 create mode 100644 test/test.R
 create mode 100644 test/test.Rmd

diff --git a/README.md b/README.md
index 411acb6..348a1a9 100644
--- a/README.md
+++ b/README.md
@@ -5,8 +5,8 @@
 Background
 =============
 
-This repositopry contains a workshop that Marcus Davy gave on 20 Feb 2014 in Palmy. Marcus used moa to steamline the analysis. This version is exactly teh same workshop except
-that it uses knitr as moe seems a wee bit out of date and not maintained these days. This versio also uses modules. If you don't have modules available (which you really should) then remove
+This repository contains a workshop that Marcus Davy gave on 20 Feb 2014 in Palmy. Marcus used moa to streamline the analysis. This version is exactly th same workshop except
+that it uses knitr as moe seems a wee bit out of date and not maintained these days. This version also uses modules. If you don't have modules available (which you really should) then remove
 the module call from your knitr scripts. As long as the system finds tassel 3 you are fine. 
 
 
@@ -15,9 +15,12 @@ Prerequisites
 
 [![Join the chat at https://gitter.im/biospectrabysequencing/gbs_rmd](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/biospectrabysequencing/gbs_rmd?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
+- wget
+- unzip
 - R (>3.1)
 - knitr
 - tassel 3
+- bowtie2
 - modules
 
 
diff --git a/test/README.md b/test/README.md
new file mode 100644
index 0000000..e691257
--- /dev/null
+++ b/test/README.md
@@ -0,0 +1,15 @@
+Testing 
+===========
+
+Executing test script
+---------------------
+
+```
+git clone https://github.com/biospectrabysequencing/gbs_rmd
+cd test
+
+Rscript test.R
+
+```
+
+
diff --git a/test/test.R b/test/test.R
new file mode 100644
index 0000000..6274f82
--- /dev/null
+++ b/test/test.R
@@ -0,0 +1,4 @@
+library(knitr)
+
+knit("test.Rmd")
+
diff --git a/test/test.Rmd b/test/test.Rmd
new file mode 100644
index 0000000..e9ea9df
--- /dev/null
+++ b/test/test.Rmd
@@ -0,0 +1,14 @@
+# Sanity checks 
+
+```{r test-bash, engine='bash'}
+
+wget -h
+unzip -h
+bowtie2 -h
+run_pipeline.pl -h
+
+pandoc test.md -o test.html
+
+```
+
+