VCRU Bioinformatics - Install notes

This page was last updated on Tuesday, 16-Dec-2014 13:03:17 CST

Installation notes for FASTX-Toolkit version 0.0.14 5-Jan-2014

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Prerequisites

libgtextutils
Either sudo apt-get install libgtextutils-dev or

$ cd /programinstallers
$ wget -N http://hannonlab.cshl.edu/fastx_toolkit/libgtextutils-0.6.1.tar.bz2
$ tar -jxvf libgtextutils-0.6.1.tar.bz2
$ cd libgtextutils-0.6.1
$ ./configure
$ make

$ sudo make install

...
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'
...

$ cd ..
Cleanup
$ rm libgtextutils-0.6.1 -rf

The fasta_clipping_histogram tool requires two perl modules: PerlIO::gzip and GD::Graph::bars.
$ sudo apt-get install libgd-dev
$ sudo apt-get install libgd-gd2-perl
$ sudo cpan GD::Text PerlIO::gzip GD::Graph::bars
The fastx_barcode_splitter tool requires GNU sed.
The fastq_quality_boxplot tool requires gnuplot version 4.2 or newer

Installation

$ ver="0.0.14"
$ cd /programinstallers/
$ wget -N https://github.com/agordon/fastx_toolkit/releases/download/$ver/fastx_toolkit-$ver.tar.bz2
$ tar -jxvf fastx_toolkit-$ver.tar.bz2
$ cd fastx_toolkit-$ver
Need following command to plocate libgtextutils if it was installed manually, skip if used apt-get
$ export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:$PKG_CONFIG_PATH
$ ./configure
$ make
$ sudo make install
$ cd ..
Cleanup
$ rm fastx_toolkit-$ver -rf