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. Best, J.