FASTX-Toolkit

FASTQ/A short-reads pre-processing tools

Download pre-compiled binaries

NOTE: precompiled binaries are provided for older version 0.0.13. Please download and compile from source code (below) for the lastest version.
Precompiled binaries availble for: Linux (64bit), Linux (32bit), OpenSolaris 2009.6, FreeBSD (64bit) MacOS X 10.5.8 (32bit)
(note: The OpenSolaris and MacOS-X binaries are dynamically linked, so they will probably not work on other versions of the operating systems)


Galaxy files (XML, test-data, static images): download

See "Galaxy Integration" section (below) for installation instructions.

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-0.0.13.tar.bz2 0.0.13 02-Feb-2010 6d233ff4ae3d52c457d447179f073a56
libgtextutils-0.6.tar.bz2 0.6 01-Dec-2009 d6969aa0d31cc934e1fedf3fe3d0dc63
fastx_toolkit-0.0.13.2.tar.bz2 0.0.13.2 26-Apr-2012 1d1238cb3029cb1c5d1a3eea7d7d2ca8
libgtextutils-0.6.1.tar.bz2 0.6.1 20-May-2011 40e7df4e5a72efe50aa789af8caeb935
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

See installation instructions for Ubuntu and Debian, OpenSolaris, CentOS/RedHat, FreeBSD,

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.

Galaxy Integration

Basic

Advanced

To use the lastest version of the fastx-toolkit tools (with all available tools), follow these steps.
A good understanding of the Galaxy system is required!

Example

##
## Download pre-compiled binaries, put them in /usr/local/bin
##
$ mkdir fastx_bin
# cd fastx_bin
$ wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
$ tar -xjf fastx_toolkit_0.0.13_binaries_Linux_2.6_amd64.tar.bz2
$ sudo cp ./bin/* /usr/local/bin

##
## Clone a fresh copy of galaxy
##
$ hg clone http://www.bx.psu.edu/hg/galaxy galaxy_test
$ cd galaxy_test
$ sh setup.sh

##
## Get the fastx-toolkit files, and extract them inside
## the galaxy directory
##
## This archive will overwrite the following files:
##   ./tools/fastx_toolkit/*
##   ./static/fastx_icons/*.png
##   ./test-data/fast{a,x,q} files
##
$ wget http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_0.0.13_galaxy_files.tar.bz2
$ tar -xjf fastx_toolkit_0.0.13_galaxy_files.tar.bz2

##
## Manually add the content of  
##   http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit_conf_0.0.13.xml.txt
## to your tool_conf.xml
##
## done!

##
## TESTING
## If you'd like to test the tools, add the content of the XML file into:
##   tool_conf.xml.sample
##
## then run:
$ sh run_functional_tests.sh -id cshl_fastq_to_fasta
$ sh run_functional_tests.sh -id cshl_fastx_renamer
$ sh run_functional_tests.sh -id cshl_fasta_formatter
$ sh run_functional_tests.sh -id cshl_fasta_nucleotides_changer
$ sh run_functional_tests.sh -id cshl_fastq_masker
$ sh run_functional_tests.sh -id cshl_fastq_quality_converter
$ sh run_functional_tests.sh -id cshl_fastq_quality_filter
$ sh run_functional_tests.sh -id cshl_fastq_quality_trimmer
$ sh run_functional_tests.sh -id cshl_fastq_to_fasta
$ sh run_functional_tests.sh -id cshl_fastx_artifacts_filter
$ sh run_functional_tests.sh -id cshl_fastx_clipper_ng
$ sh run_functional_tests.sh -id cshl_fastx_collapser
$ sh run_functional_tests.sh -id cshl_fastx_quality_statistics
$ sh run_functional_tests.sh -id cshl_fastx_renamer
$ sh run_functional_tests.sh -id cshl_fastx_reverse_complement
$ sh run_functional_tests.sh -id cshl_fastx_end_trimmer
$ sh run_functional_tests.sh -id cshl_fastx_trimmer
$ sh run_functional_tests.sh -id cshl_fastx_uncollapser
$ sh run_functional_tests.sh -id cshl_seqid_uncollapser