bfast-0.6.5a, MUMmer-3.22, and Amos-3.0.0 Installs In Ubuntu 10.04 LTS (And Related)

Taking care of a DNA/RNA fragment alignment installation triple-threat with this post. These Ubuntu installs for largely problem-free, but one little trick is needed for Amos (this because of my use of "/opt" for my usual installation and compilation attempts and, more so, my not being interested in modifying the root PATH statement despite the constant use of sudo when building in "/opt").

So, with the downloads of

bfast-0.6.5a (currently:
MUMmer-3.22 (currently:
Amos-3.0.0 (currently:

taken care of, the following process is performed.

user@machine:~sudo aptitude update
user@machine:~sudo aptitude upgrade

[POSSIBLE RESTART REQUIRED after this. You don't need-need to update/upgrade, but I do it before all builds regardless.]

user@machine:~sudo apt-get install bison build-essential cmake csh doxygen flex fort77 freeglut3-dev g++ g++-multilib gcc gcc-multilib gettext gfortran gnuplot ia32-libs lib32asound2 lib32gcc1 lib32gcc1-dbg lib32gfortran3 lib32gomp1 lib32mudflap0 lib32ncurses5 lib32nss-mdns lib32z1 libavdevice52 libbz2-dev libc6-dev-i386 libc6-i386 libfreeimage-dev libglew1.5-dev libnetcdf-dev libopenal1 libopenexr-dev libopenmpi-dev libpng12-dev libqt4-dev libssl-dev libstdc++6-4.3-dbg libstdc++6-4.3-dev libstdc++6-4.3-doc libxext-dev libxi-dev libxml-simple-perl libxmu-dev libxt-dev mercurial nfs-common nfs-kernel-server openmpi-bin patch portmap python2.6-dev rpm ssh tcsh xorg-dev zlib1g-dev

The large apt-get above is my "default" additional install for a variety of programs, including Amber, Abinit, GAMESS, GROMAC, etc. Many of these may not be needed but hard drives are cheap and figuring out the minimum list is more work than simply installing everything. Do check the list, however, to make sure something won't confuse any other installs on your machine (if you're new to this, likely not. If you've done builds a few times, you may already know the difference).

user@machine:~$ sudo mv bfast-0.6.5a.tar.gz /opt
user@machine:~$ sudo mv MUMmer3.22.tar.gz /opt
user@machine:~$ sudo mv amos-3.0.0.tar.gz /opt
user@machine:~$ cd /opt

Move the three programs to /opt (or not). Specifically for bfast, two additional apt-get's are required.

user@machine:/opt$ sudo apt-get install libstatistics-descriptive-perl libdbd-pg-perl

The build for bfast is straightforward.

user@machine:/opt$ sudo tar xvfz bfast-0.6.5a.tar.gz 
user@machine:/opt$ cd bfast-0.6.5a/
user@machine:/opt/bfast-0.6.5a$ sudo ./configure 
user@machine:/opt/bfast-0.6.5a$ sudo make
user@machine:/opt/bfast-0.6.5a$ sudo make install
user@machine:/opt/bfast-0.6.5a$ cd ..

bfast is officially built and you've returned to your "/opt" directory. MUMmer is also straightforward.

user@machine:/opt$ sudo tar xvfz MUMmer3.22.tar.gz 
user@machine:/opt$ cd MUMmer3.22/
user@machine:/opt/MUMmer3.22$ sudo make check
user@machine:/opt/MUMmer3.22$ sudo make install

MUMmer is officially built. If you intend to build Amos, you will need some of what you built in MUMmer. Specifically, nucmer, delta-filter, and show-coords are used by Amos and must be present in your PATH during the Amos build. As I am building in "/opt," I'm using sudo. As I do not want to deal with setting a new PATH for root, the solution is simply to move these three programs to a universally accessible place.

user@machine:/opt/MUMmer3.22$ sudo cp nucmer /usr/local/bin/
user@machine:/opt/MUMmer3.22$ sudo cp delta-filter /usr/local/bin/
user@machine:/opt/MUMmer3.22$ sudo cp show-coords /usr/local/bin/
user@machine:/opt/MUMmer3.22$ cd ..

And, with that, you are ready for the Amos build procedure. You will need two more apt-get installs to complete the Amos build.

user@machine:/opt/amos-3.0.0$ sudo apt-get install libboost-all-dev libqt3-headers

To build Amos with no errors and all of the listed components, note the ./configure settings and run the list below.

user@machine:/opt$ sudo tar xvfz amos-3.0.0.tar.gz 
user@machine:/opt$ cd amos-3.0.0/
user@machine:/opt/amos-3.0.0$ sudo ./configure --with-Qt-dir=/usr/share/qt3 --prefix=/opt/amos-3.0.0
user@machine:/opt/amos-3.0.0$ sudo make
user@machine:/opt/amos-3.0.0$ sudo make check
user@machine:/opt/amos-3.0.0$ sudo make install

If nucmer, delta-filter, show-coords, and the qt3 libraries are not present, you'll see the following error list after running ./configure:

-- AMOS Assembler 2.0.8 Configuration Results --
  C compiler:          gcc -g -O2
  C++ compiler:        g++ -g -O2
  GCC version:         gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /opt/amos-3.0.0
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email  with questions and bug reports.

WARNING! nucmer was not found but is required to run AMOScmp
   install nucmer if planning on using AMOScmp
WARNING! delta-filter was not found but is required to run AMOScmp-shortReads-alignmentTrimmed
   install delta-filter if planning on using AMOScmp-shortReads-alignmentTrimmed
WARNING! show-coords was not found but is required to run minimus2
   install show-coords if planning on using minimus2
WARNING! Qt3 toolkit was not found but is required to run AMOS GUIs
   install Qt3 or locate Qt3 with configure to build GUIs
   see config.log for more information on what went wrong
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)
   install Boost or locate Boost with configure to build Scaffolder
   see config.log for more information on what went wrong

And, finally, add these directories to your PATH.

user@machine:~$ cd
user@machine:~$ pico .profile

Add the following to your PATH statement:


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