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Published January 24, 2021 | Version v1.6.0
Software Open

bactopia/bactopia: v1.6.0

Authors/Creators

  • 1. Emory University
  • 2. Faculty of Computer Science, Dalhousie University

Description

v1.6.0 bactopia/bactopia "Harpoon" - 2021/01/22 Added
  • bactopia pull to pre-build Singularity images
  • --singularity_cache parameter to set location of image downloads
  • --registry to choose Docker registry to use (DockerHub, GitHub, Quay)
  • --max_downloads sets maximum number of downloads (FASTQ/assembly) allowed at once
  • --min_time sets the minimum amount of time a job should be given
  • bactopia search now uses POST requests, and groups accessions into single query
  • strip HTML from FASTA headers used in BLAST
  • Dockerfiles now have conda.md5 label to determine if rebuild is necessary
    • MD5 is updated in Dockerfile when env is updated
  • AMRFinder+ database is now provided by bactopia datasets
  • Parameterized profile (slurm, awsbatch, etc...) variables
  • bactopia build
    • will retry in case of HTTP connection issues
    • --include_tool will build Bactopia Tool environments
  • GitHub Actions
    • build Docker containers on new release (or manual trigger)
    • test that the Conda environment yamls are still valid
    • test bactopia with conda on Linux and OSX
    • test bactopia on Linux with Docker and Singularity
Fixed
  • redundant environment version files
  • failed FASTQ/Assembly downloads no longer stop whole run
  • --max_retry is honored now
  • antimicrobial_resistance process honors amrdir variable
  • change directory antimicrobial_resistance to antimicrobial-resistance
  • rename check_staging.py to check-staging.py for consistency
  • Bactopia not producing valid exit code on failure
Removed
  • --containerPath variable is replaced by --singularity_cache
  • Native Singularity recipes, will now convert Docker to Singularity
  • docs are now on bactopia.github.io repo

Files

bactopia/bactopia-v1.6.0.zip

Files (45.1 MB)

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md5:6b289249018371564a43a6ee7f53fb37
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Additional details

Related works

Is supplement to
https://github.com/bactopia/bactopia/tree/v1.6.0 (URL)