Merge branch 'singularity' into dev

Author: owlang

README.md

@@ -11,6 +11,7 @@ Scripts are generically categorized within semi-descriptive tabs and are designe
 Open **ScriptManager-Tutorial.docx** available in root directory
 
 ## Build Instructions
+### From source
 (after cloning this repo):
 ```
 $ cd scriptmanager
@@ -19,8 +20,15 @@ $ ./gradlew build
 
 The compiled JAR file will be output into the `build/libs` directory. 
 
+### Singularity
+```
+$ cd scriptmanager
+$ singularity build --fakeroot scriptmanager.sif scriptmanager.def
+```
+
 ## Running ScriptManager
 
+### .jar file
 To run the GUI verson of ScriptManager, you can double click the compiled JAR file or run the followinug command in the terminal
 ```
 $ java -jar /path/to/jarfile
@@ -36,6 +44,16 @@ $ java -jar /path/to/jarfile -h
 $ java -jar /path/to/jarfile coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
 ```
 
+### Singularity
+```
+$ singularity exec scriptmanager.sif scriptmanager ${command}
+```
+
+**Example:**
+```
+$ singularity exec scriptmanager.sif scriptmanager coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
+```
+
 ## Current scripts available (210106):
 
 **BAM Statistics:**

scriptmanager.def

@@ -0,0 +1,13 @@
+Bootstrap: docker
+From: bitnami/minideb:latest
+
+%post
+    apt-get -y update
+    apt-get -y install default-jre git
+    git clone https://github.com/CEGRcode/scriptmanager.git
+    cd scriptmanager
+    ./gradlew build
+    apt-get -y remove git
+    echo '#!/bin/bash\njava -jar /scriptmanager/build/libs/'$(ls /scriptmanager/build/libs) '"$@"' > /usr/bin/scriptmanager
+    chmod +x /usr/bin/scriptmanager
+    cd /