Setting up the environment

First step is to setup the environment in a way such that reproducibility is ensured or maximized. In this tutorial we will use the conda environment manager to install python, pyrpipe and the required tools and dependencies into a single environment. Note: Conda must be installed on the system. For help with setting up conda, please see miniconda.

Create a new conda environment

To create a new conda environment with python 3.8 execute the following commands. We recommend sharing conda environment files with pipeline scripts to allow for reproducible analysis.

conda create -n pyrpipe python=3.8

Activate the newly created conda environment and install required tools

conda activate pyrpipe
conda install -c bioconda pyrpipe star=2.7.7a sra-tools=2.10.9 stringtie=2.1.4 trim-galore=0.6.6 orfipy=0.0.3 salmon=1.4.0

To create a yaml file containing information about the conda environment, run the following command

conda env export | grep -v "^prefix: " > environment.yml

To recreate the conda environment in the environment.yml, use

conda env create -f environment.yml

We have also provided a utility to install required RNA-Seq tools via a single command:

pyrpipe_diagnostic build-tools

Note Users must verify the versions of the tools installed in the conda environment.

Setting up NCBI SRA-Tools

After installing sra-tools, please configure prefetch to save the downloads the the public user-repository. This will ensure that the prefetch command will download the data to the user defined directory. To do this

• Type vdb-config -i command in terminal to open the NCBI SRA-Tools configuration editor.
• Under the TOOLS tab, set prefetch downloads option to public user-repository

Users can easily test if SRA-Tools has been setup properly by invoking the following command

pyrpipe_diagnostic test