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
From: Thyssen, Gregory - ARS Sent: Tuesday, February 05, 2013 10:38 AM To: 'galaxy-dev@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 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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