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Requirements

System Requirements

The workflow can be launched on a Linux system, such as CentOS 7 or later (GLIBC ≥2.17) with Java 11 (or later). For running the pipeline, the recommended minimal configuration is 64 GB of RAM and 12 CPU cores. For smaller datasets, 32 GB of RAM and 6 CPU cores can be sufficient. The workflow requires temporary storage for intermediate files, ranging up to 3 TB for large (e.g. NovaSeq S4) sequencing runs.

Install Nextflow

To install the pipeline on a new system, first install Nextflow, following the instructions at https://www.nextflow.io/. The installation requires Java version 11 or higher. Once downloaded to your system, you can confirm that the Nextflow executable works as expected by running the following command:

nextflow run hello

Note that Nextflow can be installed in your user directory without admin rights on the system. Once you have the Nextflow command running, it is recommended to add the install location to the path variable in the users bash startup file (i.e., .bash_profile, .bashrc, .profile).

Install the ScaleBio Seq Suite: RNA Pipeline

The pipeline can be downloaded by two methods:

  1. By going to the ScaleBio Seq Suite: RNA GitHub page, clicking the green “Code” button and then “Download ZIP”. Then move the .zip archive to the workstation intended to run the nextflow workflow and unpack. If you unpack and then transfer the contents of the repo to another workstation the permissions for the executables will likely be stripped. One way to make sure the download is complete, check the permissions of the Python files (.py extension) in the ScaleRna/bin directory have the appropriate execute privileges on your server.

  2. The GitHub repository can be cloned to your machine:

git clone https://github.com/ScaleBio/ScaleRna.git

Determine a dependency install method

The workflow requires several dependencies and the -profile parameter controls how Nextflow manages and installs dependencies. This allows users flexibility depending on their systems requirements or limitations. All of these dependency options as well as instructions on how to enable are listed in the Dependencies section.

Need Help?

For more information, please contact support@scale.bio or visit our support website.