We need to check for avaliablility of important software packages before we run the analysis
- Java: Open command line environment and type
java --version
If version is displayed, then your system contains java. Keep in mind that the software packages would run best using the javac 11.0.8
openjdk 11.0.8 2020-07-14
OpenJDK Runtime Environment (build 11.0.8+10-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.8+10-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)
If java is not found, install using command line
sudo apt-get update
sudo apt-get install default-jre
- curl: To check whether curl is installed
curl --version
If version information is not displayed, install curl using
sudo apt-get install curl
- Miniconda3: A bootstrap version of Anaconda for python packages, to check if conda is installed
conda -V
If version information is not displayed, then install (for a 64-bit system)
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
Follow on-screen instructions until the installation is complete
Add conda to PATH
source ~/.bashrc
If the installation is successful, you should see a list of installed packages with
conda list
If the command cannot be found, add conda to PATH environment manually, open the bashrc file and add the export PATH command to the end of the file and save it.
sudo nano ~/.bashrc
export PATH=~/miniconda3/bin:$PATH
- BioPython: Package for running bioinformatics data analysis
To check if biopython is installed, run
pip list | grep biopython
If version is not returned, install using,
pip install biopython
We will be installing the following software packages in our environment to run the pipeline. Version info. is also displayed which was used to run this pipelime
- MAFFT v7.471 (2020/Jul/3)
- iqtree (multicore version 2.0.3 for Linux 64-bit built Apr 26 2020)
- jalview (2.11.1.0)
- figtree (v1.4.4)
We will add the specific channels to our conda environment before installation, and install packages using a single bash script
bash packages.sh
Once all packages are installed the pipeline can be executed using the bash script
bash pipeline.sh
The code working has been described in the documented version of the project
- Winfred Gatua (Kenya)
- Pawan Verma (India)
- Harinath. S (India)
- Ahmed El-Gammal (Egypt)
- Caroline Vilas Boas De Melo (Brazil)
- Maruf Ahmed Bhuiyan (Bangladesh)
- Oluwasefunmi Shodunke (Nigeria)
- Peter Josiah Aminu (Nigeria)
- Tracy-Allen Ezechukwu (Nigeria)
Pawan Verma
Email: pawan12394@gmail.com
Twitter: @VP_312