I partially answered my own questions by reading the Tool Dependencies wiki page.

I installed velvet to my workstation.

When I open the shell to start galaxy, I modify $PATH to include the velvet directory.

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,

Thanks,

Greg

 

 

 

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

error

An error occurred running this job:Unable to run velveth: No such file or directory

 

7: Abyss on data 5

error

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 /home/galaxy/galaxy-dist/database/files/000/dataset_9.dat

 

8: MIRA contigs (FASTA)

error

An error occurred running this job: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/3e7eca1f5d04/mira_assembler/tools/sr_assembly/mira.py", line 33, in mira_ver = get_version() File "/home/galaxy/shed_tool

 

 

15: Singleton reads reads for velvet

error

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 directory

 

 

Thanks,

Greg