manifest:
  name: waldronlab/metagenomics
  version: 1.0.0
  commands:
  - command: abi-dump
    docker_image: waldronlab/sratoolkit
  - command: abi-load
    docker_image: waldronlab/sratoolkit
  - command: align-info
    docker_image: waldronlab/sratoolkit
  - command: bam-load
    docker_image: waldronlab/sratoolkit
  - command: blastn_vdb
    docker_image: waldronlab/sratoolkit
  - command: cache-mgr
    docker_image: waldronlab/sratoolkit
  - command: cg-load
    docker_image: waldronlab/sratoolkit
  - command: curatedMetagenomicData_pipeline.sh
    docker_image: waldronlab/curatedmetagenomics
  - command: dump-ref-fasta
    docker_image: waldronlab/sratoolkit
  - command: fasterq-dump
    docker_image: waldronlab/sratoolkit
  - command: fastq-dump
    docker_image: waldronlab/sratoolkit
  - command: fastq-load
    docker_image: waldronlab/sratoolkit
  - command: helicos-load
    docker_image: waldronlab/sratoolkit
  - command: humann3
    docker_image: waldronlab/curatedmetagenomics
  - command: humann3_databases
    docker_image: waldronlab/curatedmetagenomics
  - command: humann_renorm_table
    docker_image: waldronlab/curatedmetagenomics
  - command: humann_test
    docker_image: waldronlab/curatedmetagenomics
  - command: illumina-dump
    docker_image: waldronlab/sratoolkit
  - command: illumina-load
    docker_image: waldronlab/sratoolkit
  - command: kar
    docker_image: waldronlab/sratoolkit
  - command: kdbmeta
    docker_image: waldronlab/sratoolkit
  - command: latf-load
    docker_image: waldronlab/sratoolkit
  - command: merge_metaphlan_tables.py
    docker_image: waldronlab/curatedmetagenomics
  - command: metaphlan
    docker_image: waldronlab/curatedmetagenomics
  - command: pacbio-load
    docker_image: waldronlab/sratoolkit
  - command: prefetch
    docker_image: waldronlab/sratoolkit
  - command: rcexplain
    docker_image: waldronlab/sratoolkit
  - command: remote-fuser
    docker_image: waldronlab/sratoolkit
  - command: run_markers2.py
    docker_image: waldronlab/curatedmetagenomics
  - command: sam-dump
    docker_image: waldronlab/sratoolkit
  - command: sff-dump
    docker_image: waldronlab/sratoolkit
  - command: sff-load
    docker_image: waldronlab/sratoolkit
  - command: sra-blastn
    docker_image: waldronlab/sratoolkit
  - command: sra-pileup
    docker_image: waldronlab/sratoolkit
  - command: sra-search
    docker_image: waldronlab/sratoolkit
  - command: sra-sort
    docker_image: waldronlab/sratoolkit
  - command: sra-sort-cg
    docker_image: waldronlab/sratoolkit
  - command: sra-stat
    docker_image: waldronlab/sratoolkit
  - command: sra-tblastn
    docker_image: waldronlab/sratoolkit
  - command: srapath
    docker_image: waldronlab/sratoolkit
  - command: sratools
    docker_image: waldronlab/sratoolkit
  - command: srf-load
    docker_image: waldronlab/sratoolkit
  - command: strainphlan
    docker_image: waldronlab/curatedmetagenomics
  - command: tblastn_vdb
    docker_image: waldronlab/sratoolkit
  - command: test-sra
    docker_image: waldronlab/sratoolkit
  - command: vdb-config
    docker_image: waldronlab/sratoolkit
  - command: vdb-copy
    docker_image: waldronlab/sratoolkit
  - command: vdb-decrypt
    docker_image: waldronlab/sratoolkit
  - command: vdb-dump
    docker_image: waldronlab/sratoolkit
  - command: vdb-encrypt
    docker_image: waldronlab/sratoolkit
  - command: vdb-lock
    docker_image: waldronlab/sratoolkit
  - command: vdb-passwd
    docker_image: waldronlab/sratoolkit
  - command: vdb-unlock
    docker_image: waldronlab/sratoolkit
  - command: vdb-validate
    docker_image: waldronlab/sratoolkit