ashedpotatoes/sranwrp repository overview

⁠SRAnwrp

SRAnwrp ("Saran Wrap") envelops several SRA-related tools in the warm, polyethylene embrace of a single Docker image. For the sake of simplicity, releases on main follow the same versioning scheme as the Docker image.

⁠Where?

You can find the Docker image at ashedpotatoes/sranwrp⁠. You can find a WDL task in tasks/pull_from_SRA.wdl⁠ and a WDL workflow in workflows/pull_from_SRA_simple.wdl⁠.

⁠WDL?

More information here.⁠

⁠What's Included?

Non-exhaustive list:

• bedtools-latest⁠
• bcftools-1.16⁠
• cpan-latest
• curl-latest
• entrez-direct-latest⁠ (aka edirect)
• fd-latest⁠ (aka fd-find)
• gcc-latest
• htslib-1.16⁠
• make-latest
• pigz-latest⁠
• python-3.10
• samtools-1.16⁠
• sra-tools-3.0.0⁠ (aka SRAtools, SRA tools, SRA toolkit, etc)
  • align-info, fastq-dump, fasterq-dump, prefetch, sam-dump, sra-pileup, etc
  • Note that ncbi/ncbi-vdb⁠ was merged with sra-tools in sra-tools-3.0.0
• sudo-latest
• tree-latest
• vim-latest
• wget-latest

⁠Why?

• Docker Hub's latest version of staphb/sratoolkit, as of my writing this in October 2022, runs version 2.9.2 (see command 15)⁠, which doesn't work at all anymore⁠
• Existing Docker images tend to contain either the SRA toolkit or Entrez Direct, not both
• Building SRA Toolkit on your own, without conda, is not intuitive
• Building SRA Toolkit on your own, with conda, is also not intutive (you usually end up with v2.10 which only sometimes works⁠)
• No need to run vdb-config --interactive or any other interactive process before using anything in this image; SRA Toolkit's config file is generated while building the image