AMOS on Ubuntu

By Iddo on April 19th, 2010

AMOS is a suite of genome assembly and editing software. It includes assemblers, validation, visualization, and scaffolding tools. I have been having some issues installing AMOS on Ubuntu 9.10. Specifically, Ubuntu 9.10 has gcc 4.4, which breaks the compilation of the AMOS release version. However, the development version has been fixed to accommodate that.

If you don’t know which Ubuntu version you are running, type:

$ lsb_release -a

No more than fifteen minutes after I posted my Q to the amos-help mailing list, Florent Angly came through with a solution. I am posting his email here.

Hi,

This issue was fixed in the development version of AMOS. See below for instructions on how to install this version on Ubuntu:

Download either the regular or development version of AMOS. As of April 4, 2010,
Minimo is only available from the development version of AMOS.
i/ The regular AMOS version is available from http://sourceforge.net/projects/amos/files/, e.g.:
$ wget http://sourceforge.net/projects/amos/files/amos/2.0.8/amos-2.0.8.tar.gz/download
ii/ The development version of AMOS is in a CVS repository. To get it, run:
$ cvs -z3 -d:pserver:anonymous@amos.cvs.sourceforge.net:/cvsroot/amos co -P AMOS

In the directory where the AMOS file are located, run the following to install
the prerequisites:
$ sudo aptitude install ash coreutils gawk gcc automake mummer mummer-doc libboost-dev

For the Hawkeye component of AMOS, you need Qt3:
$ sudo aptitude install libqt3-headers

For the standard version of AMOS, skip to next step, but for the CVS development version, first, run:
$ ./bootstrap

Then regardless of the version:
$ ./configure –with-Qt-dir=/usr/share/qt3 –prefix=/usr/local/AMOS
$ make
$ make check
$ sudo make install
$ sudo ln -s /usr/local/AMOS/bin/* /usr/local/bin/

Now all the programs shipped in AMOS should be available from the command-line.
For example try:
$ Minimo -h
Regards,

Florent

You will need the AMOS development version for Ubuntu 9.10 (and above, presumably), but the regular version for 9.04 (and below). If you are getting the development version, you will also need to install cvs on your machine: