Linux Software Installation – Exercises 1

Part 1. Setup Conda

1.1 Login to the BioHPC machine and download the installer

Login (ssh) to the machine that you are assigned for this workshop (assigned machines: Prepare the working directory, and download the latest version of Miniconda/python3 installer into the working directory.

mkdir /workdir/$USER
cd /workdir/$USER


1.2 Run the installer

chmod u+x 


1.3 Miniconda is ready.

Part 2. Install and run a simple software in Conda

2.1 Install bwa in Conda

source $HOME/miniconda3/bin/activate
conda install -c bioconda bwa


2.2 Run bwa in Conda

Next time you login, to run bwa that you installed:

source $HOME/miniconda3/bin/activate
which bwa


Part 3. Work with Conda environment

3.1 Create a virtual environment and give it a name “pysam”, install pysam the virtual environment

conda create -c bioconda -n pysam pysam


3.2 Start the pysam environment, and run python

conda activate pysam
which python
python -V
which pip

3.3 Install other python modules in this environment

 pip install numpy


3.4 End the environment

conda deactivate

3.5. Now you installed pysam and numpy in miniconda3 in the home directory. Next time you need to use it in a new session, run these commands

source $HOME/miniconda3/bin/activate
conda activate pysam
# after the work is done
conda deactivate

Part 4. Create a Python2.7 environment in Miniconda3

conda create -n myNewPipeline python=2.7
conda activate myNewPipeline
which python
python -V    ##use  capital V
conda deactivate 

Note in the first command there is no package name. This step would create an empty python2.7 environment, within which you can use pip to install other python modules.