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Question: Error: Unable to access jarfile /please/GenomeAnalysisTK.jar
0
gravatar for Mic
3.4 years ago by
Mic • 70
Australia
Mic • 70 wrote:
Hello, I tried to use Depth of Coverage (version 2.8.0), but I got the following error:

Error: Unable to access jarfile /please/GenomeAnalysisTK.jar
mv: cannot stat `/galaxy/galaxy-dist/database/files/000/dataset_93.dat.sample_summary': No such file or directory

How is it possible to fix the above error?

Thank you in advance,

Mic

 

 

 
galaxy • 2.0k views
ADD COMMENT • link •
modified 3.4 years ago by Bjoern Gruening ♦ 5.1k • written 3.4 years ago by Mic • 70
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

we are not allowed to ship the JAR file, because of licensing issues. You need to download it by yourself and specify the location in the env.sh file in you GATK Tool Shed installation directory.

Sorry,

Bjoern
 
ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Hi, by any chance do you know where the env.sh file is located. Thank you in advance.

ADD REPLY • link written 3.4 years ago by Mic • 70

Somewhere in tool_deps/gatk/iuc/gatk/ ...

ADD REPLY • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Unfortunately, there is no such file in galaxy-dist/shed/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/

ADD REPLY • link written 3.3 years ago by Mic • 70

Not in shed_tools, here all TS informations are stored. You need to look in tool_deps where all your compiled dependencies are stored.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k
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