Install Fastx (zz)

Fastx-toolkit installation on CentOS
=====================================

Tested on CentOS release 5.3 (FINAL) x86_64

Prerequisites:
  pkg-config, gcc, g++, wget
 
Using YUM, install gcc, g++, pkg-config and wget

 $ sudo yum install pkgconfig.x86_64 gcc.x86_64 gcc-c++.x86_64 wget.x86_64
 
Verify GCC/G++ versions - must be atleast 4.1

 $ gcc -v
 Using built-in specs.
 Target: x86_64-redhat-linux
 Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
 Thread model: posix
 gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
 

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 ..
 
 // Tell pkg-config to look for libraries in /usr/local/lib, too.
 $ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH  ##### This is very IMPORTANT!!!!!!!!!!!!
 //
 // 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.

 

 

Original Link  http://hannonlab.cshl.edu/fastx_toolkit/install_centos.txt