manifest:
  name: databio/lab_geofetch
  version: 1.0.0
  imports:
  - bulker/alpinebase:default
  commands:
  - command: ascp
    docker_image: quay.io/biocontainers/aspera-cli:4.20.0--hdfd78af_0
    docker_command: ascp
  - command: aws
    docker_image: mesosphere/aws-cli
  - command: bamtools
    docker_image: quay.io/biocontainers/bamtools:2.5.1--he860b03_5
  - command: bedtools
    docker_image: quay.io/biocontainers/bedtools:2.29.0--hc088bd4_3
  - command: bigWigAverageOverBed
    docker_image: quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h199ee4e_0
  - command: bismark
    docker_image: quay.io/biocontainers/bismark:0.22.1--0
  - command: bissnp
    docker_image: quay.io/biocontainers/bis-snp:1.0.1--2
  - command: bsmap
    docker_image: quay.io/biocontainers/bsmap:2.90--he860b03_2
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.17--pl5.22.0_2
  - command: cufflinks
    docker_image: quay.io/biocontainers/cufflinks:2.2.1--py27_2
  - command: curl
    docker_image: curlimages/curl:7.69.1
    docker_command: curl
    docker_args: -i
  - command: fastq-dump
    docker_image: quay.io/biocontainers/sra-tools:2.10.0--pl526he1b5a44_0
    docker_command: fastq-dump
  - command: geofetch
    docker_image: databio/geofetch
    docker_args: -i
    docker_command: geofetch
  - command: hisat2
    docker_image: quay.io/biocontainers/hisat2:2.0.4--py35_0
  - command: homer
    docker_image: quay.io/biocontainers/homer:4.10--pl526hc9558a2_0
  - command: kallisto
    docker_image: quay.io/biocontainers/kallisto:0.42.4--2
  - command: macs2
    docker_image: quay.io/biocontainers/macs2:2.2.6--py37h516909a_0
  - command: pigz
    docker_image: nsheff/pigz
    docker_command: pigz
    docker_args: -i
  - command: prefetch
    docker_image: quay.io/biocontainers/sra-tools:2.10.0--pl526he1b5a44_0
    docker_command: prefetch
  - command: R
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_10
    docker_command: R
    docker_args: -it --volume=${HOME}/.local/lib/R:/usr/local/lib/R/host-site-library
  - command: rg
    docker_image: peccu/rg
  - command: Rscript
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_10
    docker_command: Rscript
    docker_args: -it --volume=${HOME}/.local/lib/R:/usr/local/lib/R/host-site-library
  - command: salmon
    docker_image: combinelab/salmon:1.0.0
  - command: sambamba
    docker_image: quay.io/biocontainers/sambamba:0.7.1--h148d290_0
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.24--hc9558a2_3
  - command: samtools
    docker_args: -i
    docker_image: quay.io/biocontainers/samtools:1.9--h91753b0_8
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--h2d50403_2
  - command: trim_galore
    docker_image: quay.io/biocontainers/trim-galore:0.6.5--0
  - command: trimmomatic
    docker_image: quay.io/biocontainers/trimmomatic:0.35--6