This is an overview of how to download the pipeline
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Overview

Downloading the pipeline is as simple as using Git, or using the GitHub website.
Several things will be downloaded during this section:

  1. The pipeline itself
  2. Conda (and Mamba)

Pipeline Download

First-time Download

Using Git

  1. In a terminal, log in to the cluster (if you are using one)
  2. Navigate to the directory where you would like to download the pipeline (i.e., cd /work/helikarlab/joshl)
  3. Execute the following command to download the pipeline: 
    git clone https://github.com/HelikarLab/FastqToGeneCounts.git

You can now navigate into the downloaded directory and run the pipeline.

Using GitHub

  1. Navigate to the GitHub repository
  2. Click the green “Code” button, which looks like this: GitHub Code Button
  3. Click Download ZIP, and follow the prompts (if any) to download the pipeline.
  4. Unzip the downloaded file
  5. Once this is done, you must upload this directory onto the cluster (if you are using one)
    1. It is recommended to use a cluster, as the STAR aligner has high memory requirements.
    2. You should upload into the appropriate “work” directory (i.e., /work/helikarlab/joshl)
  6. You can now navigate into the directory (on the cluster) and run the pipeline

Updating the Pipeline

  1. In a terminal, navigate to the directory where you downloaded the pipeline.
  2. Execute the following command to update the pipeline: 
    git pull

Unfortunately, there is no easy method of updating the pipeline strictly using the GitHub website. It is recommended to use Git to update.

If any errors occur during the update process, please open an issue on our GitHub page for assistance.

Conda Download

Nearly every cluster has conda installed. If you are running this in an environment that does not have conda installed (such as a local computer), please follow the instructions here to download and install conda for your system: https://docs.conda.io/en/latest/miniconda.html

This installation will use MiniConda, which is a slim version of Conda, capable of installing the necessary software for the pipeline.