> I hope I have the correct place to ask for assistance.

Yes, this list is a great place to ask questions about local Galaxy instances.

> I've been trying to use a local install of Galaxy. I can upload data and 
> convert formats (FASTq to FASTA) but can't use fasta manipulation tools like 
> width formatter or collapse. I am told "No such file or directory /bin/sh: 
> fasta_formatter: command not found". I don't see these in the list of tools 
> with dependencies. I've used them frequently on the public website so I don't 
> think this is a problem of my file formats. What am i missing? When I try to 
> send a bug report through the local I get an error that mail is not 
> configured. 

You need to install analysis tools that you want to use with Galaxy. The tool 
shed will help with some tools (see Admin --> Tool sheds --> search and browse 
tool sheds), but others you'll have to install yourself by downloading them and 
adding them to your PATH.

> I tried to do the local install because my files on the web version have been 
> sitting for many hours waiting to run.

There was a problem with our public server's cluster, but it's been fixed and 
jobs should be running more quickly now.

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