Simile on Ubuntu 12.04 LTS (Precise)

Installing Simile on a Linux box using a package management system is usually pretty straightforward, but there are a couple of issues that cause problems if you are using this popular release of Ubuntu. Oddly they are unique to 12.04 LTS (Precise) -- they do not occur on earlier or later Ubuntu versions.

Firstly, this distro does not include the tk-table package. Simile depends on this to display tabular data, in the table I/O tool and when editing file data for parameters. An easy solution was found by one of our customers -- add the bio-linux repository from NERC Environmental Bioinformatics Centre to your software sources. This can be done in a terminal:

sudo add-apt-repository ppa:nebc/bio-linux

sudo apt-get update

This repository contains the tk-table package in a compatible form, as well as many other useful things.

The other problem is a bit harder to diagnose. The Ubuntu 12.04 LTS repository includes a buggy version of the tcl-trf package. This package is used by Simile to encode and decode its saved files as MIMEs and to generate and check authentication strings for saved models. The buggy version cannot be loaded into the Tcl shell, the result is that Simile fails to start, producing this error:

unknown command "::md5"

The evaluation edition will start (no licence code to check!) but fail to load or save models, producing an error message containing the above line.

The package has been fixed (by Debian) but the Precise repository has not been updated with the fixed version . So you need to get the version from the Quantal (subsequent Ubuntu release) repository. You get the 32-bit version from this page:

https://launchpad.net/ubuntu/quantal/i386/tcl-trf/2.1.4-dfsg-3

-- link to tcl-trf_2.1.4-dfsg-3_i386.deb
 

This is the 32-bit version. If you are using a 64-bit distribtion, replace i386 with amd64 in the above address. This package is compatible with Precise and once it is installed, Simile should work normally.