Fastx-toolkit installation on FreeBSD
=====================================

Tested on FreeBSD release 8.0-RELEASE

Prerequisites:
  pkg-config, gcc, wget
 
Using the ports collection, install pkg-config and wget:

 # cd /usr/ports/devel/pkg-config
 # make install
 # cd /usr/ports/ftp/wget
 # make install
 
Verify GCC/G++ versions - must be atleast 4.2

 $ gcc -V
 Using built-in specs.
 Target: amd64-undermydesk-freebsd
 Configured with: FreeBSD/amd64 system compiler
 Thread model: posix
 gcc version 4.2.1 20070719  [FreeBSD]
 


Fastx-Toolkit Installation:

 //
 // Install libgtextutils
 //
 $ wget http://cancan.cshl.edu/labmembers/gordon/files/libgtextutils-0.6.tar.bz2
 $ tar -xjf libgtextutils-0.6.tar.bz2
 $ cd libgtextutils-0.6
 $ ./configure
 $ make
 $ sudo make install
 $ cd ..
 
 //
 // Install fastx-toolkit
 //
 $ wget http://cancan.cshl.edu/labmembers/gordon/files/fastx_toolkit-0.0.12.tar.bz2 
 $ tar -xjf fastx_toolkit-0.0.12.tar.bz2 
 $ cd fastx_toolkit-0.0.12
 $ ./configure
 $ make
 $ sudo make install
 
 
Sanity check:

 //
 // run fastx_uncollapser without full path,
 // should find the executable in /usr/local/bin and also
 // be able to find /usr/local/lib/libgtextutils-0.6.so
 $ fastx_uncollapser -h
 usage: fasta_uncollapser [-c N] [-h] [-v] [-i INFILE] [-o OUTFILE]
 Part of FASTX Toolkit 0.0.12 by A. Gordon (gordon@cshl.edu)

  [-h]         = This helpful help screen.
  [-v]         = verbose: print short summary of input/output counts
  [-c N]       = Assume input is a tabular file (not FASTA file),
		 And the collapsed identifier (e.g. '1-1000') is on column N.
  [-i INFILE]  = FASTA/Tabular input file. default is STDIN.
  [-o OUTFILE] = FASTA/Tabular output file. default is STDOUT.