Ian,

To assist tracking down this issue, could you provide the output of the following commands?


uname -m
uname -s

   --Dave B.

On 12/20/2013 08:43 AM, UMD Bioinformatics wrote:
Hello Devteam,

I’ve just updated my local instance to the latest version. With the migration 
of tools to the tool shed I used the migrate command to keep my tools as they 
were in the previous versions.

$ sh ./scripts/migrate_tools/0008_tools.sh install_dependencies

and I’ve updated the database to 117

$ sh manage_db.sh upgrade

However, when I’m using samtools I’m getting an error related to the data. I’m 
not sure what the issue is and I’ve check all the .loc and .sh files and 
everything is pointing to the proper locations. Any ideas what the issue might 
be?

An error occurred with this dataset:Could not determine Samtools version /bin/sh: line 
1: 1616 Segmentation fault: 11 samtools 2>&1 Error extracting alignments from 
(/galaxy-dist/database/files/001/dataset_1585.dat),

Cheers
Ian


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