Thursday, May 23, 2013

Biomart 0.8 :: Ant :: Build Failed

$ git clone https://github.com/biomart/biomart-rc6.git
biomart-rc6/
$ cd biomart-rc6/
$ ant
:
[mkdir] Created dir: /home/user/Desktop/biomart-rc6/dist/registry/linkindices
:

BUILD FAILED
/home/user/Desktop/biomart-rc6/build.xml:33: Unable to find a javac compiler;
com.sun.tools.javac.Main is not on the classpath.
Perhaps JAVA_HOME does not point to the JDK.
It is currently set to "/usr/lib/jvm/java-7-openjdk-amd64/jre"

On Linux machine when I installed openjdk, it had only installed jre.
To install jdk from openjdk

$ sudo apt-get install openjdk-7-jdk

I rerun the ant command
$ ant
BUILD SUCCESSFUL

Wednesday, May 1, 2013

BioMart 0.8 :: ant :: Build Failed

Follow the step as mentioned in BioMart 0.8 User manual

$ git clone https://github.com/biomart/biomart-rc6.git
biomart-rc6/
$ cd biomart-rc6/
$ ant
:
[mkdir] Created dir: /home/user/Desktop/biomart-rc6/dist/registry/linkindices
:
BUILD FAILED
/home/user/Desktop/biomart-rc6/build.xml:137: /home/user/Desktop/biomart-rc6/registry/linkindices does not exist.

Unable to find a fix on the internet
- Since I know the linkindices directory was created.
- I opened the file build.xml
- Change the entry at line number 138 from
<fileset dir="${basedir}/registry/linkindices" includes="*"/>
- To
<fileset dir="${basedir}/dist/registry/linkindices" includes="*"/>

I rerun the ant command
$ ant
BUILD SUCCESSFUL

It worked