Pre requirements

1. Python 3 (https://www.python.org/). Barapost is tested on Python interpreter version 3.8.1.

Barapost is written in Python 3X and won't work on Python 2X.

2. BLAST+ toolkit is used by "barapost-local.py" for creating a database and aligning.

   It can be downloaded here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

   Installation:

   • Linux: download tarball, unpack it and add bin/ directory from unpacked tree to PATH variable. (this should also work for macOS)

   • Windows: download .exe executable, run it and follow installation. Do not forget to add "BLAST+" to PATH during installation (you will see corresponding checkbox at one of installation steps). It is a trap with BLAST+ 2.10.0 on Windows, we recommend to use BLAST+ 2.9.0 (see Using on Windows) for details.

   "barapost-local.py" has been tested on Linux and Windows with BLAST+ version 2.10.0.

3. h5py Python package is used by "barapost-binning.py" for binning FAST5 files.

   This package is not necessary if you don't intend to bin FAST5 files.

   On Linux, libhdf5-dev is required to build h5py.

   Installation:

   • Linux (assumming that your packet manager is apt and you use pip3 as Python package installer):

     sudo apt install libhdf5-dev
     pip3 install h5py
     

   Binning FAST5 files have been tested on Linux and Windows (h5py version 3.8.0 was used).