Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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

Installation notes for amos version 3.1.0rc2

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Prerequisites

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