How to install Java and JavaWS in Linux

Last night I’ve learnt Oracle changed the Java licensing which broke all channels of installation typically used in Linux.

Still, you can obtain & install Java and JavaWS free-of-charge manually for personal and developmental use. This is how to proceed:

cd ~/Download
tar xpfz jre-8u211-linux-x64.tar.gz
  • Move folder to `/opt/java`
sudo mkdir -p /opt/java
sudo mv jre1.8.0_211 /opt/java
  • Remove or rename symbolic links if they exists
which java
which javaws
ls -la /usr/bin/java*
sudo rm /usr/bin/java*
  • Link new java version
sudo ln -s /opt/java/jre1.8.0_211/bin/java /usr/bin/java
sudo ln -s /opt/java/jre1.8.0_211/bin/javaws /usr/bin/javaws

Now everything should work just fine 🙂

Installing Gene Cluster on Ubuntu

Gene Cluster is a program for clustering. I wanted to use it to analyse gene expression data. However, I had problems during installation under Ubuntu 14.04. This is how I solved it:

# install dependencies: Motif libraries
sudo apt-get install libxext-dev libmotif-dev

Get GeneCluster3.0 source code and unpack it.

# configure to install in local dir
./configure --prefix=`pwd` --program-prefix=gene_ && make && make install

# add install dir to ~/.bashrc

pysam installation error on Ubuntu 14.04

If you encounter error during pysam installation:

sudo easy_install -U pysam

... 

pysam/csamtools.c:8:22: fatal error: pyconfig.h: No such file or directory
 #include "pyconfig.h"
                      ^
compilation terminated.
error: Setup script exited with error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

try installing python-dev first.

sudo apt-get install python-dev

Solution found on github.