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