This page was last updated on Friday, 28-Nov-2014 12:32:35 CST

Installation notes for jvarkit version xxx

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Prerequisites

Java 1.7

ant
$ sudo apt-get install ant

Installation

https://github.com/lindenb/jvarkit/wiki/Compilation

1. $ cd /usr/local/bin/
2. $ git clone https://github.com/lindenb/jvarkit.git
3. $ cd jvarkit
4. $ git submodule init
5. $ git submodule update
6. $ cd htsjdk
7. $ ant clean
8. $ ant
9. $ cd ..
10. Programs are compiled individually, e.g.
    $ cd /usr/local/bin/jvarkit
11. $ ant sam4weblogo
    …
    [jar] Building jar: /usr/local/bin/jvarkit/dist/sam4weblogo.jar
    …
12. And it can be run with e.g.
    $ java -jar /usr/local/bin/jvarkit/dist/sam4weblogo.jar