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