Owen Hardy wrote:
Hi,
I set up a local instance on OS 10.6 and was using some fasta tools but noticed fasta width formatter does not execute. Although it shows in my local web interface I do not see width formatter in the tools.conf.xml, nor does the python script appear in /tools/fasta_tools with the others. I also browsed source from central and dist in fasta_tools and do not see it there either...Thanks for any help.
An error occurred running this job:/bin/sh: fasta_formatter: command not found zcat: /Users/Owen/Galaxy/galaxy-dist/database/files/000/dataset_190.dat.Z: No such file or directory
Hi Owen,
Galaxy has various external dependencies for which it provides wrappers - this is one of them, namely, the FASTX-Toolkit, available here:
http://hannonlab.cshl.edu/fastx_toolkit/
If you install the Toolkit and insure that it's on your $PATH (i.e. you can run 'fasta_formatter' on the command line), using it in Galaxy should work.
--nate
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