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
Requirements
- Fastx-toolkit version 0.0.13 requires libgtextutils-0.6 (available here for download)
- A recent g++ compiler (tested with GNU G++ 4.1.2 and later).
- The fasta_clipping_histogram tool requires two perl modules: PerlIO::gzip and GD::Graph::bars.
- The fastx_barcode_splitter tool requires GNU sed.
- The fastq_quality_boxplot tool requires gnuplot version 4.2 or newer.
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
- The current Galaxy repository already contains some of the fastx-toolkit tools.
- If you just want to use the existing tools, simply download the pre-compiled binaries, put them in /usr/local/bin (or any accessible path), and Galaxy will be able to run these tools.
- Note that not all the tools are enabled in tool_conf.xml.
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!
- Download the pre-compiled binaries, or compile the programs from source.
- Put binaries in /usr/local/bin (or other accessible path)
- Copy the fastx-toolkit Galaxy files into to your Galaxy directory.
NOTE:This will overwrite some of galaxy's existing fastx-toolkit files.
- Add the fastx-toolkit tools to your tool_conf.xml file (List of tools).
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