POLYSOLVER Installation

The installation for Polysolver requires downloading dependencies from external sources and providing the path to each dependency in the config.sh file within polysolver.

In the case of GATK, which is one of Polysolver's dependencies it is unclear how to set the path. In the polysolver shell script, "shell_call_hla_typ.sh", it points to a GATK file, $GATK_DIR/CollectInsertSizeMetrics.jar, but CollectInsertSizeMetrics.jar is not a file within the GATK download. This is also the case for $GATK_DIR/SamToFastq.jar.

Can someone provide instruction on the proper config.sh environment path to provide for GATK as part of the polysolver installation?

Hey ericg, I know it's an old

Hey ericg,

I know it's an old post, but if you're still humting, the picard-tools jars used to be individual tools. Try extracting https://github.com/broadinstitute/picard/releases/download/1.120/picard-... to somewhere on your system and point the GATK_DIR environment variable in the config.sh and/or config.bash (depending on which shell your users prefer) to where you extracted it.

I'm pretty sure you can go as new as picard-tools-1.23.zip, but we had a 1.120 and it ran.