Summary and Setup

Setup

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Two scenarios:

• JAX: No setup required. Just need sumner access & terminal program.
• Outside:
  • install nextflow (beyond scope),
  • configure nextflow profile for local computing environment,
  • install Singularity (will Docker work?),
  • get Singularity containers from ???,
  • get reference files Zenodo,

Data Sets

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If you are working outside of The Jackson Laboratory, you will need to download the reference FASTA and GTF file from: Zenodo.

Specifically, you should download:

• Ensembl 105 GTF
• GRCm39 FASTA
• GRCm39 FASTA Index

You should also download the mouse SNP and Indel files from the Mouse Genomes Proejct.

• SNP VCF
• SNP VCF Index
• Indel VCF
• Indel VCF Index

Software Setup

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Details

You will be using a terminal window to connect to your computing cluster via secure shell (ssh). See the links below for different operating systems to see which program to use.

Windows

We recommend MobaXterm for connecting to external systems.

MacOS

Mac/OS has a Terminal.app that can connect to external systems.

Linux

Linux systems have a terminal and should have ssh installed to connect to external systems.