Fastx-toolkit installation on Ubuntu

Fastx-toolkit installation on Ubuntu
=====================================

Tested on Ubuntu Server 9.10 amd64

Prerequisites:
  pkg-config, gcc, wget
 
Using APT, install gcc and pkg-config

 $ sudo apt-get install gcc g++ pkg-config wget
 
Verify GCC/G++ versions - must be atleast 4.2

 $ gcc -v                                                         
 Using built-in specs.                                                           
 Target: x86_64-linux-gnu                                                        
 Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.4.1-4ubuntu8' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared --enable-multiarch --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4 --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc --disable-werror --with-arch-32=i486 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
 Thread model: posix                                                             
 gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu8)
 

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
 
 //
 // To run the fastx programs, you'll need to tell ubuntu about
 // about the new shared library in /usr/local/lib.
 //
 // Method one:
 //   add /usr/local/lib to LD_LIBRARY_PATH environment variable
 $ export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 //
 // Method two:
 // run 'ldconfig' to update the shared libraries cache
 $ sudo ldconfig
 
 
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 ([email protected])

  [-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.