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Question: Megablast is not working
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gravatar for Sandrine.Hughes
2.8 years ago by
Sandrine.Hughes • 0
European Union
Sandrine.Hughes • 0 wrote:

Hello,

I've seen in previous posts that there was some problem with the megablast tool some months ago and I would like to know if the problem was solved because the tool is not working for me. I obtain the following error message when I'm trying to use it:

python: can't open file '/galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/dc7b4acb3fa6/megablast_wrapper/megablast_wrapper.py': [Errno 2] No such file or directory
/scratch/03166/xcgalaxy/main/staging/11586263/command.sh: line 40: /galaxy-repl/main/deps/samtools/0.1.18/env.sh: No such file or directory

Thanks for your help,

Sandrine
megablast galaxy • 822 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by Sandrine.Hughes • 0
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello Sandrine,

There have been some Megablast issues, but this does not look like those. Instead, the problem is most likely an installation problem.

It looks as if SAMTool is not installed. Do that first. I would also recommend installing Picard.

The simplest way to install tools is to use Managed Dependencies. For troubleshooting, removing and reinstalling repositories (any of these) might correct the problem. Review in the Admin panel installed tools to check status, update repos, and the like. 

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 2.8 years ago • written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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