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Installing RSeQC (L14)

Installing RSeQC using Conda

Follow these steps to install RSeQC using Conda in your VACC account.

Step 1. Load Python

Before installing Conda and RSeQC, load the appropriate Python module:

module load python3.10-anaconda/2023.03-1

Step 2: Verify the Loaded Module

Check that the Python module is correctly loaded by listing active modules:

module list

Expected output:

Currently Loaded Modules:
  1) python3.10-anaconda/2023.03-1

Step 3: Confirm Python and Conda Installation

Verify that Python and Conda are available:

python --version
conda --version

Expected output:

Python 3.10.9
conda 22.9.0

Step 4: Initialize Conda for Your Shell

Run the following command to initialize Conda for your specific shell:

conda init only needs to be run once after installing Conda. If the user has already initialized Conda, they don’t need to run it again.

conda init

Then reload your shell configuration. 

exec $SHELL

Step 5: Create a Conda Environment

Create a dedicated Conda environment for RSeQC with Python 3.10:

conda create -n rseqc_env python=3.10 -y

During installation, you may see messages like:

Collecting package metadata (current_repodata.json): done
Solving environment: done

Conda will check for required dependencies. If prompted, type y to proceed:

Proceed ([y]/n)? y
  • y confirms the installation of required dependencies
  • n cancels the installation

At the end, you will see a message like this:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate rseqc_env
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Retrieving notices: ...working... done

Now, proceed to Step 5.

Step 6: Activate the rseqc_env Environment

Activate the newly created Conda environment:

conda activate rseqc_env

Once activated, your terminal prompt will change from (base) to (rseqc_env), indicating that you are inside the new environment.

[pdrodrig@vacc-login4 pdrodrig]$ conda activate rseqc_env 
(rseqc_env) [pdrodrig@vacc-login4 pdrodrig]

Step 7: Install RSeQC Using pip

With the environment activated, install RSeQC using pip:

pip install RSeQC

Once installed successfully, you should see output similar to:

Successfully installed RSeQC-5.0.4 bx-python-0.13.0

Step 8: Verify the Installation

Test the installation by displaying the help page for read_distribution.py:

read_distribution.py --help

Expected output:

Usage: read_distribution.py [options]

Check reads distribution over exon, intron, UTR, intergenic ... etc
The following reads will be skipped:
    qc_failed
    PCR duplicate
    Unmapped
    Non-primary (or secondary)

Congratulations! You have successfully installed RSeQC!

Important Notes

  • Each time you use RSeQC, you must first activate the Conda environment:
conda activate rseqc_env

  • RSeQC will not work in the base environment.

  • To deactivate the environment after use, run:

conda deactivate