Installation

Prerequisites

Fundamental prerequisites

python => v2.7.10
R => v3.4
perl => v5.10

These items are prerequisites for the installation of ShadowCaster as described below.

Packages

  • Install python packages using:
pip install numpy scipy biopython pandas ete3 scikit-learn matplotlib
  • R packages: cluster v2.0.*
  • Install figlet. For Linux (Mint 18.3) use:
apt install figlet

Other dependencies

For using the phylogenetic component, some programs are required and should be in the PATH:

  • BLAST 2.2.26+ (blastp needed).

If you have a newer version of BLAST already installed, you just can copy the path to the executable file for blastp in the configuration file of ShadowCaster.

OrthoMcl needs blast v2.2.26(blastall and formatdb), these binary files can be found here. Download blast-2.2.26-*.tar.gz.

For Linux (Mint 18.3) this can be installed through:

apt-get install blast2

More information, see Suggestions.

  • Package emboss.

For Linux (Mint 18.3) this is installed through:

apt-get install emboss

To check that these dependencies were correctly added in the path, run:

type orthomcl-pipeline blastall formatdb

Installation of ShadowCaster

To use ShadowCaster, download it from the GitHub repository and extract the files. If you have git installed, you can install ShadowCaster by running:

cd
git clone https://github.com/dani2s/ShadowCaster.git

Resolve all dependencies, see above and then execute:

cd ShadowCaster/
python setup.py install

This will install ShadowCaster under your home folder.