Hi Jeremy,

Two things confuse me about this. First, the tools I want to use are
not listed under the list of tools with dependencies.. but I still
need to install? what is the difference then between tools with
dependencies and all the others?

Second, in the instructions it suggest that nothing should be listed
under the tools when you do a local install... (the instructions I was
reading showed screen shots indicating that you configure each tool
and it appears in the left hand menu)... when I did the install
everything was listed (just not functioning). Is that normal?


On Fri, Jan 18, 2013 at 9:27 PM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
>> 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.


Dr. Elizabeth L. Clare

School of Biological and Chemical Sciences
Queen Mary, University of London
Mile End Road, London E1 4NS
Room 1.02, G. E. Fogg Building
+44 (0)207 882 ext. 5687

School of Biological Sciences
University of Bristol, Bristol, UK.
Phone: +44 117 954 5909
Website: http://seis.bris.ac.uk/~bzelc/

"If you say yes more often than you say no, you will do interesting
things in your life"

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