FASTX-Toolkit

FASTQ/A short-reads pre-processing tools

Source Code GIT Repository

libGTextUtils on Github
Fastx-Toolkit on Github

Download

File Version Release Date md5 sum
fastx_toolkit-0.0.6.tar.bz2 0.0.6 25-Feb-2009 5fa5dfa03c48db9058d1bdf8a8e04857
fastx_toolkit-0.0.7.tar.bz2 0.0.7 24-Mar-2009 41f29d9e848fc5d8b06e3a11f4fe0006
libgtextutils-0.1.tar.gz 0.1 24-Mar-2009 dbc6fd761103bb17d512bed796288de9
fastx_toolkit-0.0.8.tar.bz2 0.0.8 12-May-2009 c748a56f906cf7436ea6ee20c024ebdd
libgtextutils-0.3.tar.bz2 0.3 12-May-2009 9803edba96036a32b3b7256d4869d38b
fastx_toolkit-0.0.10.tar.bz2 0.0.10 10-Aug-2009 5a7b21e2eb467a28f6b14aabc7223f61
libgtextutils-0.5.tar.bz2 0.5 10-Aug-2009 410f9b79618799ee146587a2b71ab7b0
fastx_toolkit-0.0.11.tar.bz2 0.0.11 24-Nov-2009 a969aedd8050f509cb836209ac9cd391
fastx_toolkit-0.0.14.tar.bz2 0.0.14 5-Jan-2014
libgtextutils-0.7.tar.gz 0.7 5-Jan-2014

Requirements

Program Installation

note: libggtextutils is a static library, used by fastx-toolkit during compilation stage. If you get compilation errors regarding PKG_CONFIG or GTEXTUTILS not found, see this email for a possible solution. If you wish to install fastx-toolkit to a non-standard location (e.g. not /usr or /usr/local), see this email for tips.

First Install libgtextutils-0.5
$ tar -xzvf libgtextutils-0.5.tar.bz2
$ cd libgtextutils-0.5
$ ./configure
$ make
$ make check
$ sudo make install

Then, install fastx-toolkit
$ tar -xjvf fastx_toolkit-0.0.11.tar.bz2
$ cd fastx_toolkit-0.0.11
$ ./configure
$ make
$ sudo make install

Galaxy Integration

Galaxy integration is only relevant if you're running your own local Galaxy server, as explained in the Galaxy Wiki.

Integrating the FASTX-Toolkit into Galaxy requires some manual tweaking of Galaxy's configuration files.
More information can be found in the README file.

A script named install_galaxy_files.sh in the FASTX-Toolkit directory copies the necessary XML files to the Galaxy's tools folder.
Then, you'll need to update the tool_conf.xml file and add the FASTX-toolkit tools to your Galaxy configuration.

Assuming you've installed the galaxy server in /home/gordon/galaxy_dist, run the following command:

$ cd fastx_toolkit-0.0.11
$ ./install_galaxy_files.sh /home/gordon/galaxy_dist/

FASTX-toolkit Galaxy Installation script.

Checking Galaxy destination directory...ok
Checking FASTX-toolkit source directory...ok
Creating static/fastx_icons directory...OK
Copying static/fastx_icons...OK
Copying test-data files...OK
Copying tool-data files...OK
Creaing tools/fastx_toolkit directory...OK
===
=== NOTE:
===
If the FASTX-toolkit XML files already exist on your galaxy server,
   You will be prompted to confirm overwriting them.
   If you have made any changes to the XML files, DO NOT overwrite your files.

   Copying FASTX-toolkit XML tool configuration...ok
   FASTX-toolkit files copied to your galaxy server directory.

   Additionally, you'll need to make the following manual configurations:

   1. Add the content of 
   ./galaxy/fastx_toolkit_conf.xml 
   to
   /home//gordon/galaxy_dist//tool_conf.xml

   2. Update the adapters file:

   /home/gordon/galaxy_dist/tool-data/fastx_clipper_sequences.txt

   And add valid adapters/linkers.

   3. Edit "fastx_barcode_splitter_galaxy_wrapper.sh", change 
   The two variables BASEPATH and PUBLICURL to valid path/URL.
   See README for detailed explanation (under the
   "Special configuration for Barcode-Splitter" section).