module load  bioinformatics/fastx-toolkit/0.0.13

module display  bioinformatics/fastx-toolkit/0.0.13
-------------------------------------------------------------------


/sw/com/modulefiles/bioinformatics/fastx-toolkit/0.0.13:

module-whatis    FASTX-Toolkit provides command-line tools pre-processing short-reads in FASTA and FASTQ files
prepend-path     PATH /sw/fastx-toolkit/fastx/0.0.13/bin
prepend-path     C_INCLUDE_PATH /sw/fastx-toolkit/libgtextutils/0.6/include/gtextutils
prepend-path     LD_LIBRARY_PATH /sw/fastx-toolkit/libgtextutils/0.6/lib
prepend-path     LIBRARY_PATH /sw/fastx-toolkit/libgtextutils/0.6/lib
module           load compiler/gcc-4.5.2


-------------------------------------------------------------------

Software Requirements
=====================

1. GCC is required to compile most tools.

2. FASTA-Clipping-Histogram tool requires Perl, the "PerlIO::gzip",
   "GD::Graph::bars" modules.

   Installing the perl modules can be accomplised by running:

   $ sudo cpan 'PerlIO::gzip'
   $ sudo cpan 'GD::Graph::bars'

3. FASTX-Barcode-Splitter requires the GNU Sed program.

4. FASTQ-Quality-Boxplot and FASTQ-Nucleotides-Distribution requires the
   'gnuplot' program.



Installation
============

To compile to tools, run:

  $ ./configure
  $ make

To install the tools, run (as root):

  $ sudo make install

This will install the tools into /usr/local/bin.
To install the tools to a different location, change the 'configure' step to:

  $ ./configure --prefix=/DESTINATION/DIRECTORY

yum install perl-PerlIO-gzip
yum install perl-GDGraph
yum install gnuplot

Download the following and installed them to satisfy this requirement:

(gnuplot-4.2.6-2.el6.x86_64.rpm         perl-GD-2.44-3.el6.x86_64.rpm       perl-GDTextUtil-0.86-15.el6.noarch.rpm
gnuplot-common-4.2.6-2.el6.x86_64.rpm  perl-GDGraph-1.44-7.el6.noarch.rpm  perl-PerlIO-gzip-0.18-6.el6.x86_64.rpm)


mkdir -p /sw/bioinformatics/FASTX-Toolkit/0.0.13/src/fastx_toolkit-0.0.13
cd /sw/bioinformatics/FASTX-Toolkit/0.0.13/src/fastx_toolkit-0.0.13
bunzip2 fastx_toolkit-0.0.13.tar.bz2
tar -xvf fastx_toolkit-0.0.13.tar

bunzip2 libgtextutils-0.6.tar.bz2
tar xvf libgtextutils-0.6.tar
cd /sw/bioinformatics/FASTX-Toolkit/0.0.13/src/fastx_toolkit-0.0.13
mv ../libgtextutils-0.6 .

cd /sw/bioinformatics/FASTX-Toolkit/0.0.13/src/fastx_toolkit-0.0.13
./configure --prefix=/sw/bioinformatics/FASTX-Toolkit/0.0.13 2>&1 | tee configure-fastx-toolkit.txt
make 2>&1 | tee make-fastx-toolkit.txt
make install 2>&1 | tee make_install-fastx-toolkit.txt