Paths for Software Porting

This chapter lists software installation paths involved in the GATK software porting.

**Table 1** Paths for software porting
No.	Software Installation Path	Description	Remarks
1	-	Installation path of each software package for setting up the basic environment	See "Paths for Software Porting" in Basic Environment Setup Guide.
2	/path/to/BLAT	Installation path of BLAT	The installation paths listed in this table are only examples. Shared paths are recommended. Replace the paths used in commands in this document with the actual paths planned during the installation process.
3	/path/to/BMA	Installation path of BMA
4	/path/to/SAMTOOLS	Installation path of Samtools
5	/path/to/GATK	Installation path of GATK

Parent topic: GATK 4.0.0.0 Porting Guide (CentOS 7.6)