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Downloading VGP genomes using awscli

By Tanya Lama

Table of Contents

Install

  1. install or module load anaconda and awscli/1.16.144
    I have installed awscli on Unity following the instructions here: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html

module load awscli-v2/2.15.53

  1. navigate to the mSorAra bucket. This includes the mito assembly, curated genome assemblies, raw data (genomic_data) and transcriptomic data
    /home/tlama_umass_edu/.local/bin/aws s3 –no-sign-request ls s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/
  2. Copy the uncurated assembly to your local directory.
    /home/tlama_umass_edu/.local/bin/aws s3 –no-sign-request cp s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra1.pri.asm.20211103.fasta.gz ./

Appendix and FAQ

Find this document incomplete? Leave a comment!

tags: VGP

where did myoNig go?
not here:
/work/pi_tlama_umass_edu/project_toga/genomes/hg38/trackData
/work/tlama_umass_edu/project_toga/genomes/hg38/trackData

partial here:
/work/tlama_umass_edu/project_bat1k_longevity/analyses/step3_annotation/myoNig_bill

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Tanya Lama
As a molecular ecologist I use population genomic data to explore the ecology of species of conservation concern.
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