Regrettably, 454’s GS De Novo Assembler, known more commonly as Newbler, only officially supports Red Hat Enterprise Linux 4 and 5. Thankfully, with a dash of command-line wizardry, it’s possible to run version 2.8 of Assembler in Ubuntu 12.04 (and also, I imagine, more recent versions such as Ubuntu 12.10 and Ubuntu 13.04). The method I see commonly referenced requires the user run a great many commands and do much mucking about. Based on one of the succeding posts in the aforelinked thread, however, I found a much simpler method.
Much of the difficulty in running the application on Ubuntu arose because my Ubuntu installation is 64-bit. Though Assembler supposedly supports both 32-bit and 64-bit architectures, the included JVM used for the application’s Java-based GUI requires several 32-bit libraries. Once they are installed, the rest of the process is straightforward.
# Install 32-bit version of libs needed for JRE packaged with Newbler
apt-get install libxi6:i386 libxtst6:i386
# Extract assembler archive downloaded from 454
tar xvzf DataAnalysis_2.8_All_20120731_2108.tgz
cd DataAnalysis_2.8_All/packages/
# Extract RPMs
for foo in *.rpm; do rpm2cpio $foo | cpio -idmv; done
cd opt/454/apps
# Run assembler
assembly/bin/gsAssembler
The only aggravating part of this process was figuring out what 32-bit libraries were required. When I ran gsAssembler, it originally issued this error:
Exception in thread "main" java.lang.UnsatisfiedLinkError:
.../DataAnalysis_2.8_All/packages/opt/454/apps/jre/jre1.6.0_30/lib/i386/xawt/libmawt.so:
libXext.so.6: cannot open shared object file: No such file or directory
Figuring out what package contained this file was simply a matter of searching for libXext.so.6 on Ubuntu’s excellent package directory.