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Question: map with bwa-mem error
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gravatar for Marc
3.6 years ago by
Marc • 30
United Kingdom
Marc • 30 wrote:

Could not determine BWA version Traceback (most recent call last): File "/Users/shed_tools/toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/ebb02ba5987c/bwa_mem/bwa_mem.py", line 262, in <module> __main__() File "/Users/yihui/Desktop/shed_

when I try to run my local galaxy to use this tool(Map with BWA-MEM), I run into this problem. Does anyone know how to fix it?
bwa galaxy map • 1.3k views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by Marc • 30
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gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

When you installed from the Tool Shed, did you use "managed dependencies" within the admin tool forms? Have you double checked the list of installed tools to see if there were any problems/the install was complete?

I realize that these seem obvious, but are sometimes easy to miss, especially if you have installed many tools.

The error is not exactly clear - but please be aware that this tool requires reference genomes and indexes to function. There are Data Managers in the Tool Shed for these functions. Be sure to create SAM indexes for every genome - many tools/functions reply on that content.

Thanks and let us know if this extra info does not help. We will need more details about your instance and the full error report/log to diagnose this further. Best, Jen, Galaxy team

 
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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