When apt-get magic fails and ‘java-package’ cannot be found, here is how to install J2SE(TM) Runtime Environment 5.0 Update 9 on your AMD64 Ubuntu 6.10 system. Download the appropriate JRE for your architecture and type the following:

% cd /usr/local/lib

% sh /tmp/jre-1_5_0_09-linux-amd64.bin

% cd /usr/local/bin

% ln -sf ../lib/jre1.5.0_09/bin/* .

% java -version

java version “1.5.0_09″
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)
Java HotSpot(TM) 64-Bit Server VM (build 1.5.0_09-b03, mixed mode)

No magic here.

I’ve installed the latest version of Sun Microsystems Gridengine product (N1GE 6.0u8) on our 64-bit Ubuntu LINUX dedicated processing host for 454 assemblies. In the absence of assembly benchmark or production data, I’ve installed the latest version of the NCBI toolkit (blast, et alia), an rsync process from our target repository and submitted a couple of BLAST test sets to the system as a test.

% qstat -f
queuename                      qtype used/tot. load_avg arch          states
----------------------------------------------------------------------------
all.q@merge.kunaufamily.org       BIP   4/4       3.68     lx24-amd64
      1 0.55500 BLAST      kunau        r     11/02/2006 21:30:35     1 60
      1 0.55500 BLAST      kunau        r     11/02/2006 21:31:05     1 63
      1 0.55500 BLAST      kunau        r     11/02/2006 21:31:20     1 64
      1 0.55500 BLAST      kunau        r     11/02/2006 21:31:35     1 65

############################################################################
 - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS
############################################################################
      1 0.55500 BLAST      kunau        qw    11/02/2006 21:04:44     1 66-100:1
      2 0.55500 BLAST      kunau        qw    11/02/2006 21:32:03     1 1-3455:1

They appear to be running as expected.

The data and binary paths are the same as those on our ROCKS clusters. This should make it possible for our users to run any of their working scripts on this new system. Nothing new here.