Question: Error: Unable to access jarfile /please/GenomeAnalysisTK.jar
0
gravatar for Mic
3.4 years ago by
Mic70
Australia
Mic70 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 COMMENTlink modified 3.4 years ago by Bjoern Gruening5.1k • written 3.4 years ago by Mic70
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k 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 COMMENTlink written 3.4 years ago by Bjoern Gruening5.1k

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

ADD REPLYlink written 3.4 years ago by Mic70

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

ADD REPLYlink written 3.4 years ago by Bjoern Gruening5.1k

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

ADD REPLYlink written 3.3 years ago by Mic70

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 REPLYlink written 3.3 years ago by Bjoern Gruening5.1k
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