Preparing your system
LSTrAP is designed with High Performance Computing in mind and requires a computer cluster running Oracle Grid Engine or PBS / Torque. Furthermore, the essential tools (see below) need to be installed prior to running LSTrAP. Using the Environment modules are supported, in that case the configuration file needs to contain the exact names of the modules containing the tools.
Required Tools
- Bowtie2
- TopHat
- HISAT2
- Samtools
- SRAtools
- HTSeq + all dependencies (including PySam)
- Python 3.5 + SciPy + Numpy
- MCL
- Trimmomatic
Optional tools
- InterProScan
- OrthoFinder
- Python 2.7 (for OrthoFinder)
- scikit-learn for Python 3, required for PCA analysis (helper script)
- seaborn for Python 3, required for PCA analysis (helper script)
- Aspera connect client, required for the get_sra_ip.py (helper script)