Unable to build applet in DNAnexus, .jar file not found

Question

[_quantum_girl_]

Hi I saved my .jar file in resources/usr/bin however I get this error:

Error: Unable to access jarfile SnpSift.jar  

I don't get this error with other types of binary files.

I want to run something like this:

cat input_file | java -jar SnpSift.jar filter "((ANN[*].IMPACT = 'HIGH') | (ANN[*].IMPACT = 'MODERATE'))" > output_file

Is there something that I'm doing wrong?

[GenoMax]

Please contact DNANexus support. That may be your best bet since this is commercial software and not many here will have access.

[Ram]

Ah I missed the part where DNANexus makes this problem out of our reach. Thank you, GenoMax!

Answer 1

[LChart]

The resources bundle is unpacking SnpSift.jar into /usr/bin; but it is a jar file that is executed via java.

You can either java -jar /usr/bin/SnpSift.jar which looks weird; or, alternatively, save SnpSift.jar into resources/home/dnanexus/SnpSift.jar and your command line will work, as the .jar file will be unpacked into the execution home directory.

Answer 2

[Ram]

That's not how $PATH works. Place your jar file in any accessible location, then add a script to your /usr/local/bin like so:

#!/bin/sh 
java -jar /path/to/SnpSift.jar "$*"

Name this script 'snpsift`. Then you'll be able to do this:

cat input_file | snpsift filter "((ANN[*].IMPACT = 'HIGH') | (ANN[*].IMPACT = 'MODERATE'))" > output_file