How to run 454's GS De Novo Assembler (Newbler) v2.8 in Ubuntu 12.04

Jeff Wintersinger
by Jeff Wintersinger
July 24, 2013

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.


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