Hello Greg,

For the repositories you've listed I believe you'll have to manually install the dependencies and make sure they can be located within the user account that you use to start your Galaxy server. You can contact the repository owners using each repository's pop-up menu if you have questions about dependencies - see below. Some of the tool dependency requirements are documents in README files within the repository, but not every repository includes them.

Another place to look for requirements is the View tool metadata pop-up menu.

The page displayed from the above menu option may include information about required tool dependencies.

Greg Von Kuster

On Feb 5, 2013, at 11:37 AM, Thyssen, Gregory - ARS wrote:

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

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