I partially answered my own questions by reading the Tool Dependencies wiki 
I installed velvet to my workstation.
When I open the shell to start galaxy, I modify $PATH to include the velvet 
Now the error I get in  Velvet suggests it found the program, but something 
else is wrong.

My new error is:
No reads found

The reads are fastq files that appear in my history and are data libraries 
housed in an external harddrive.
I have used these same data before on the public server.

Please advise,

From: Thyssen, Gregory - ARS
Sent: Tuesday, February 05, 2013 10:38 AM
To: 'galaxy-...@bx.psu.edu'
Subject: Velvet program files

So I am setting up my local Galaxy on a workstation for my own use.
I have installed several programs from the Assembly Main Tool Shed.
None works.
Are these just the wrappers?  Do I need to install, say, Velvet somewhere 
outside of Galaxy?
How do I do this?

My errors:
6: velveth on data 2
An error occurred running this job:Unable to run velveth: No such file or 

7: Abyss on data 5
An error occurred running this job: ERROR: Expected exactly 3 arguments; got: 
67 /media/My Passport/IM-Data2Bio-10262012/IM-mut1/Im-mutant-bulk_1.fastq 

8: MIRA contigs (FASTA)
An error occurred running this job: Traceback (most recent call last): File 
 line 33, in mira_ver = get_version() File "/home/galaxy/shed_tool

15: Singleton reads reads for velvet
An error occurred running this job: Error running preppereads.sh /bin/sh: 
/users/galaxy/galaxyscripts/prepare_pe_reads_for_velvet.sh: No such file or 


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