Install

To use TrioMix, first install it using git:

$ git clone https://github.com/cjyoon/triomix.git

To verify installation, you can use the following commands. If everything is setup correctly, the following commands should result in the TrioMix help menu being printed in your terminal.

$ cd triomix
$ python triomix.py -h

Dependencies

TrioMix is written in Python (v3.5 or later) and R. Following Python and R packages are used in TrioMix.

Python
- pysam
- pandas
R
- optparse
- tidyverse
- bbmle
- PSCBS

Other dependencies

TrioMix internally uses samtools, Rscript, and gzip. Make sure these are in your $PATH. Otherwise, you can edit the absolute path of each of these in path_config.json.

$ cat path_config.json
{"SAMTOOLS": "/path/to/samtools", # default is 'samtools'
 "RSCRIPT": "/path/to/Rscript", # default is 'Rscript'
 "GZIP": "/path/to/gzip" # default is 'gzip'
}

Using the docker images

Pre-built docker image with all prerequisites installed is available.

$ docker pull cjyoon/triomix