How to compile 'JVARKIT'

JVARKIT_compliation

# run 'blastn' (-outfmt 5 --> XML outformat)
$ for p in ./*pa.fa; 
do  
blastn -outfmt 5 \
       -query hg_normal_ensembl_cancerGenes_mRNA \
       -subject $p \
       -out $p.blast; 
done 


# install java 1.8 (java 8)
$ sudo add-apt-repository ppa:webupd8team/java
$ sudo apt-get update
$ sudo apt-get install oracle-java8-installer


# set java 1.8 (java 8) as a defualt
$ sudo update-alternatives --config java

There are 3 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
* 0            /usr/lib/jvm/java-8-oracle/jre/bin/java          1074      auto mode
  1            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1071      manual mode
  2            /usr/lib/jvm/java-7-oracle/jre/bin/java          1073      manual mode
  3            /usr/lib/jvm/java-8-oracle/jre/bin/java          1074      manual mode

Press enter to keep the current choice[*], or type selection number: 

# select appropriate one. '0' in this case.
$ java -version
java version "1.8.0_66"
Java(TM) SE Runtime Environment (build 1.8.0_66-b17)
Java HotSpot(TM) 64-Bit Server VM (build 25.66-b17, mixed mode)


# install 'apache ANT'
$ sudo apt-get install ant xsltproc 



# download 'jvarkit' @ https://github.com/lindenb/jvarkit/archive/master.zip
$ unzip jvarkit-maters
$ cd jvarkit-masters
$ make blastn2snp  # to install balstn2snp