Fastx-toolkit installation on OpenSolaris
=====================================

Tested on OpenSolaris release 2009.6

Prerequisites:
  pkg-config, gcc >= 4.2, wget
 
Using the Package Manager GUI, install the following packages:
  gcc-432
  gcc-runtime-432
  SUNWgnome-common-devel  (for 'pkg-config')

Verify GCC/G++ versions - must be atleast 4.3
  
 //
 // Important note:
 // the default gcc that comes with OpenSolaris 2009.6 is version 3.4.3 (csl-sol210-3_4-20050802)
 // fastx-toolkit requires a newer version of GCC.
 $ ls /usr/bin/gcc*
 /usr/bin/gcc /usr/bin/gcc-4.3.2 /usr/bin/gccbug /usr/bin/gccbug-4.3.2
 $ gcc-4.3.2 -v
 Using built-in specs.
 Target: i386-pc-solaris2.11
 Configured with: ../gcc-4.3.2/configure --prefix=/usr --program-suffix=-4.3.2 --infodir=/usr/share/info --mandir=/usr/share/man --libexecdir=/usr/lib --enable-shared --disable-static --disable-libtool-lock --target= --enable-objc-gc --enable-concept-checks --disable-libada --enable-libssp --enable-languages=c,c++,objc,fortran --enable-threads=posix --enable-tls=yes --with-system-zlib --without-gnu-ld --with-ld=/usr/ccs/bin/ld --with-gnu-as --with-as=/usr/sfw/bin/gas --with-gmp-include=/usr/include/gmp --with-gmp-lib=/usr/lib --with-mpfr-include=/usr/include/mpfr --with-mpfr-lib=/usr/lib --enable-c99 --enable-nls --enable-wchar_t --enable-libstdcxx-allocator=mt --with-pic
 Thread model: posix
 gcc version 4.3.2 (GCC) 


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
 //
 // NOTE: This is the critical step:
 // forcing both GCC and G++ versions by overriding the environment variables.
 //
 $ CC=gcc-4.3.2 CXX=g++-4.3.2 ./configure
 $ make
 $ sudo make install
 $ cd ..
 
 //
 // Install fastx-toolkit
 //
 $ wget 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
 
 // Tell pkg-config to look for libraries in /usr/local/lib, too.
 $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
 //
 // NOTE: This is the critical step:
 // forcing both GCC and G++ versions by overriding the environment variables.
 //
 $ CC=gcc-4.3.2 CXX=g++-4.3.2 ./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.