This page was last updated on Thursday, 10-Jul-2014 14:37:29 CDT

Installation notes for amos version 3.1.0rc2

Home Page

Prerequisites

• automake
  Ubuntu: $ sudo apt-get install autotools-dev automake
• qt development version
  Fedora: $ sudo yum install qt-devel
  Ubuntu: $ sudo apt-get install libqt4-dev
• Boost graph toolkit is required to run parts of the AMOS Scaffolder (Bambus 2)
  Ubuntu: $ sudo apt-get install libboost-graph-dev
• Perl modules used by AMOS
  $ sudo cpan XML::Parser Config::IniFiles Statistics::Descriptive DBI
• MUMmer
• BLAT
• Jellyfish version 1.1.x (2.x not supported?) if using --with-jellyfish flag to configure
• In the past, under Fedora, I did not have a qmake but I had qmake-qt4, this fixed the problem
  $ sudo ln -s /usr/bin/qmake-qt4 /usr/bin/qmake

Installation

1. $ cd /programinstallers/
2. The version on the download page is not actually the most current, and there are bugs there. See http://seqanswers.com/forums/archive/index.php/t-17770.html
   
3. To get the current version 3.1.0rc2
   $ git clone git://git.code.sf.net/p/amos/code amos-code
4. $ cd amos-code
5. $ ./bootstrap
6. $ ./configure --prefix=/usr/local/AMOS
7. If an error occurs of the format

         WARNING! nucmer was not found but is required to run AMOScmp and minimus2
      install nucmer if planning on using these programs

   set appropriate environment variable before running configure, e.g.
   $ export NUCMER=/usr/local/bin/MUMmer/nucmer
   

   Some influential environment variables:
     PERL        perl command
     PYTHON      python command
     NUCMER      nucmer command
     DELTAFILTER delta-filter command
     SHOWCOORDS  show-coords command
     BLAT        blat command
     CXX         C++ compiler command
     CXXFLAGS    C++ compiler flags
     LDFLAGS     linker flags, e.g. -L if you have libraries in a
                 nonstandard directory 
     LIBS        libraries to pass to the linker, e.g. -l
     CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I if
                 you have headers in a nonstandard directory 
     CC          C compiler command
     CFLAGS      C compiler flags
     CPP         C preprocessor
     XMKMF       Path to xmkmf, Makefile generator for X Window System

8. (Obsolete, Version 3.1.0 only): A fix for the error find-tandem.cc:243:3: error: ‘optarg’ was not declared in this scope
   from http://seqanswers.com/forums/showthread.php?t=17802
   $ nano src/Align/find-tandem.cc
   ... include this after line #9
   #include <getopt.h>
   ...
9. $ make CXXFLAGS='-Wno-deprecated'
10. $ sudo make install
11. Add to the default PATH for all users
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/AMOS/bin"
    ...
12. Cleanup
    $ cd .. ; rm amos-code -rf