Or at least changing "zcat" to "cat" in your XML files, as
"zcat" on Mac-OS behaves differently than linux's (and that is the source of
your error message).
Nate Coraor wrote, On 05/11/2011 10:22 AM:
Owen Hardy wrote:
> 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
Galaxy has various external dependencies for which it provides wrappers
- this is one of them, namely, the FASTX-Toolkit, available here:
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
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