Dear Community,
I am from system-administrator side, and totally new in this field about bio-informatic, so excuse my weird question.
I am attempting to reproduce results of:
Nature Biotechnology 33, 1152–1158 (2015) doi:10.1038/nbt.3344
http://archive.broadinstitute.org/cancer/cga/polysolver
The main issue is that they do not provide the exact versions of the used tools, neither git commits.
Now, (at least) 2 years after, it is (unfortunately) almost impossible to re-launch --as-is-- their test-cases and there is some errors, just because the User-Interface of such tools have evolved (hopefully! ;-).
I do not want to re-write and/or adapt polysolver to the current and latest versions of the tools, just re-run the published software.
Well, I have read some Release Notes, trying to identify the versions. But, at some point, it is unfruitful... and too painful!
One of there errors is about GATK, i.e., polysolver claims:
Error: Unable to access jar file path/to/gatk/SamToFastq.jar
Where do I find SamToFastq.jar ?
Does it move to Picard ?
If yes, now it seems that the UI is not SamToFastq.jar but java -jar path/to/picard/picard.jar <tool-name> .... Therefore, what is the last version of Picard considering the previous UI ?
Or maybe, I am not able to correctly read the documentation and I miss a point.
Thank you in advance for any advice !
All the best!