Hello,
A new version of FASTX-Toolkit is available for download at http://hannonlab.cshl.edu/fastx_toolkit/download.html
This version should be much easier to integrate with galaxy.
New tools: fastq_masker (suggested by Ben Bimber) New features: fastx_trimmer can trim N nucleotides from the end of the sequences (a new command line option, and a separate tool in Galaxy) fastx_clipper accepts minimum adapter length to clip (requested by Erick Antezana, command line only) Improved Galaxy integration: Almost all tools have working functional tests (except the plotting tools and barcode splitter). Plotting tools (nucleotide distribution and quality boxplot) detect input file type and show a detailed warning if given a FASTA/Q file as input (hopefully reducing bug reports). Tools read the input FASTQ type (sanger or solexa) and use the correct quality ASCII offset (33 for sanger, 64 for solexa).
Comments are welcomed, -gordon