Installation#

System requirements#

Software dependency

  • python >= 3.6.0

  • pytorch >= 1.12.0

  • pybedtools >= 0.9.0

  • gffutils >= 0.10.0

  • pybind11 >= 2.10.0

Version warning

Splam is currently not compatible with the latest version of python=3.11.4 due to a dependency issue with pybedtools. We are currently investigating and will patch in a future update. In the meantime, we recommend running in a python=3.10 environment, as shown below

$ conda create -n myenv python=3.10


There are three ways that you can install Splam:

Install through pip#

Splam is on PyPi 3.12 now. Check out all the releases here. Pip automatically resolves and installs any dependencies required by Splam.

$ pip install splam

Install from source#

You can also install Splam from source. Check out the latest version on GitHub !

$ git clone https://github.com/Kuanhao-Chao/splam --recursive

$ cd splam/src/

$ python setup.py install

Install through conda#

Installing Splam through conda is the easiest way to go:

TBC

$ conda install -c bioconda splam

Check Splam installation#

Run the following command to make sure Splam is properly installed:

$ splam -h
Terminal output
====================================================================
An accurate spliced alignment pruner and spliced junction predictor.
====================================================================


███████╗██████╗ ██╗      █████╗ ███╗   ███╗
██╔════╝██╔══██╗██║     ██╔══██╗████╗ ████║
███████╗██████╔╝██║     ███████║██╔████╔██║
╚════██║██╔═══╝ ██║     ██╔══██║██║╚██╔╝██║
███████║██║     ███████╗██║  ██║██║ ╚═╝ ██║
╚══════╝╚═╝     ╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝

usage: splam [-h] [-v] [-c] {extract,score,clean} ...

splice junction predictor to improve alignment files (BAM / CRAM)

optional arguments:
-h, --help            show this help message and exit
-v, --version
-c, --citation

Commands:
{extract,score,clean}
    extract             Extracting all splice junctions from an alignment or annotation file
    score               Scoring all splice junctions
    clean               Cleaning up spurious splice alignment

Now, you are ready to go !#

Please continue to the Quick Start Guide.