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3. Loading RNAseq environment

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Akshay Paropkari edited this page Apr 7, 2022 · 3 revisions

RNAseq pipeline is implemented in a Conda environment called RNA-seq. Conda enables virtual environments that contain the required software packages/libraries to be installed and set up. In this instance, the RNAseq conda environment contains the BBMap suite, STAR alignment software, and FASTQC tool. Besides, required Python and R libraries and their dependencies are also installed.

After logging into the MERCED cluster, you will need to activate the RNA-seq Conda environment. Run the following commands to activate the environment -

module load anaconda3
source activate RNA-seq

You will see the activated environment path in parenthesis at your prompt as such -

(/opt/anaconda_shared_envs/RNA-seq)[<username>@merced ~]$

Alternatively, users can use the rnaseq.yml file to install the environment locally, as such -

cd RNA-seq/
conda env create -f rnaseq.yml

# After conda finishes installing the environment, run the following to activate it -
conda activate rnaseq

Table of contents

  1. Introduction
  2. Accessing MERCED cluster
  3. Loading RNAseq environment
  4. Creating input data folder
    1. Transferring data to/from MERCED to a local machine
  5. Running RNAseq pipeline as a MERCED job
    1. Overview
    2. Required changes to the job template file
    3. Example of changed job template file
    4. Submitting jobs to MERCED
  6. Output files

Quick Access

  1. Introduction
  2. Accessing MERCED cluster
  3. Loading RNAseq environment
  4. Creating input data folder
    1. Transferring data to/from MERCED to a local machine
  5. Running RNAseq pipeline as a MERCED job
    1. Overview
    2. Required changes to the job template file
    3. Example of changed job template file
    4. Submitting jobs to MERCED
  6. Output files
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