manifest:
  name: bulker/biobase
  version: 0.1.18
  description: A curated collection of the most common bioinformatics command-line
    tools, containerized for use with bulker.
  imports:
  - bulker/alpine:default
  - bulker/coreutils:default
  commands:
  - command: ascp
    docker_image: quay.io/biocontainers/aspera-cli:4.20.0--hdfd78af_0
    docker_command: ascp
  - command: bamtools
    docker_image: quay.io/biocontainers/bamtools:2.5.3--he132191_0
  - command: bcftools
    docker_image: quay.io/biocontainers/bcftools:1.24--h118bc1c_2
  - command: bedClip
    docker_image: quay.io/biocontainers/ucsc-bedclip:482--h0b57e2e_0
    docker_args: -i
  - command: bedCommonRegions
    docker_image: quay.io/biocontainers/ucsc-bedcommonregions:482--h0b57e2e_0
  - command: bedGraphToBigWig
    docker_image: quay.io/biocontainers/ucsc-bedgraphtobigwig:482--hdc0a859_0
    docker_args: -i
  - command: bedIntersect
    docker_image: quay.io/biocontainers/ucsc-bedintersect:482--h0b57e2e_0
    docker_args: -i
  - command: bedItemOverlapCount
    docker_image: quay.io/biocontainers/ucsc-beditemoverlapcount:482--h0b57e2e_0
    docker_args: -i
  - command: bedops
    docker_image: quay.io/biocontainers/bedops:2.4.42--hd6d6fdc_1
  - command: bedPileUps
    docker_image: quay.io/biocontainers/ucsc-bedpileups:482--h0b57e2e_0
    docker_args: -i
  - command: bedToBigBed
    docker_image: quay.io/biocontainers/ucsc-bedtobigbed:482--hdc0a859_0
    docker_args: -i
  - command: bedtools
    docker_image: quay.io/biocontainers/bedtools:2.31.1--h13024bc_3
    docker_args: -i
  - command: bigBedToBed
    docker_image: quay.io/biocontainers/ucsc-bigbedtobed:482--h0b57e2e_0
    docker_args: -i
  - command: bigWigAverageOverBed
    docker_image: quay.io/biocontainers/ucsc-bigwigaverageoverbed:482--h0b57e2e_0
    docker_args: -i
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:482--h0b57e2e_0
    docker_args: -i
  - command: bigWigSummary
    docker_image: quay.io/biocontainers/ucsc-bigwigsummary:482--h0b57e2e_0
    docker_args: -i
  - command: bigWigToWig
    docker_image: quay.io/biocontainers/ucsc-bigwigtowig:482--h0b57e2e_0
    docker_args: -i
  - command: bismark
    docker_image: quay.io/biocontainers/bismark:3.1.0--hfa8f182_0
  - command: bissnp
    docker_image: quay.io/biocontainers/bis-snp:1.0.1--hdfd78af_3
  - command: blast
    docker_image: quay.io/biocontainers/blast:2.17.0--hb02a186_1
  - command: bowtie
    docker_image: quay.io/biocontainers/bowtie:1.3.1--hb82490e_11
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.5.5--h63e9258_1
  - command: bsmap
    docker_image: quay.io/biocontainers/bsmap:2.90--h43eeafb_5
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.19--h577a1d6_1
  - command: cellranger
    docker_image: quay.io/xujishu/cellranger:6.0.1
  - command: cufflinks
    docker_image: quay.io/biocontainers/cufflinks:2.2.1--py36_2
  - command: cutadapt
    docker_image: quay.io/biocontainers/cutadapt:5.2--py313hd978853_2
  - command: deeptools
    docker_image: quay.io/biocontainers/deeptools:4.0.0--py313h9a1e870_0
  - command: faSplit
    docker_image: quay.io/biocontainers/ucsc-fasplit:482--h0b57e2e_0
  - command: fasterq-dump
    docker_image: quay.io/biocontainers/sra-tools:3.4.1--h4304569_1
    docker_command: fasterq-dump
  - command: fastp
    docker_image: quay.io/biocontainers/fastp:1.3.6--h43da1c4_0
  - command: fastq-dump
    docker_image: quay.io/biocontainers/sra-tools:3.4.1--h4304569_1
    docker_command: fastq-dump
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0
  - command: featureCounts
    docker_image: quay.io/biocontainers/subread:2.1.1--h577a1d6_0
    docker_command: featureCounts
  - command: freebayes
    docker_image: quay.io/biocontainers/freebayes:1.3.10--h3752d28_1
  - command: gatk
    docker_image: broadinstitute/gatk:4.7.0.0
    docker_command: gatk
  - command: gt
    docker_image: quay.io/biocontainers/genometools-genometools:1.6.6--py311h21ec246_1
  - command: hisat2
    docker_image: quay.io/biocontainers/hisat2:2.2.3--h8471819_1
  - command: homer
    docker_image: quay.io/biocontainers/homer:5.1--pl5321hc52dbad_1
  - command: htseq-count
    docker_image: quay.io/biocontainers/htseq:2.1.2--py313h9d32f87_3
    docker_command: htseq-count
  - command: kallisto
    docker_image: quay.io/biocontainers/kallisto:0.52.0--hd638d68_1
  - command: liftOver
    docker_image: quay.io/biocontainers/ucsc-liftover:482--h0b57e2e_0
  - command: macs2
    docker_image: quay.io/biocontainers/macs2:2.2.9.1--py310h1fe012e_5
  - command: mashmap
    docker_image: quay.io/biocontainers/mashmap:3.1.3--pl5321hb4818e0_2
  - command: minimap2
    docker_image: quay.io/biocontainers/minimap2:2.31--h118bc1c_0
  - command: multiqc
    docker_image: quay.io/biocontainers/multiqc:1.35--pyhdfd78af_1
  - command: picard
    docker_image: broadinstitute/picard:3.5.0
    docker_command: picard
  - command: pigz
    docker_image: nsheff/pigz
    docker_command: pigz
    docker_args: -i
  - command: prefetch
    docker_image: quay.io/biocontainers/sra-tools:3.4.1--h4304569_1
    docker_command: prefetch
  - command: R
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_23
    docker_command: R
    docker_args: -it
    description: You should add --volume=${HOME}/R/4.4:/usr/local/lib/R/host-site-library
      to tool_args
  - command: refgenie
    docker_image: databio/refgenie:latest
  - command: repeatmasker
    docker_image: quay.io/biocontainers/repeatmasker:4.2.4--pl5321hdfd78af_0
  - command: Rscript
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_23
    docker_command: Rscript
    docker_args: -it
  - command: rsem-calculate-expression
    docker_image: quay.io/biocontainers/rsem:1.3.3--pl5321h077b44d_12
    docker_command: rsem-calculate-expression
  - command: salmon
    docker_image: quay.io/biocontainers/salmon:2.7.0--hfa8f182_0
  - command: sambamba
    docker_image: quay.io/biocontainers/sambamba:1.0.1--he614052_4
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.26--h9948957_7
  - command: samtools
    docker_image: quay.io/biocontainers/samtools:1.24--h9dcdb79_1
    docker_args: -i
  - command: seqkit
    docker_image: quay.io/biocontainers/seqkit:2.13.0--he881be0_0
  - command: seqtk
    docker_image: quay.io/biocontainers/seqtk:1.5--h577a1d6_1
    docker_args: -i
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--hc9558a2_3
  - command: STAR
    docker_image: quay.io/biocontainers/star:2.7.11b--h5ca1c30_8
  - command: stringtie
    docker_image: quay.io/biocontainers/stringtie:3.0.3--h29c0135_0
  - command: tabix
    docker_image: quay.io/biocontainers/htslib:1.24--ha79157c_0
  - command: trim_galore
    docker_image: quay.io/biocontainers/trim-galore:2.3.0--hf1b6044_0
  - command: trimmomatic
    docker_image: quay.io/biocontainers/trimmomatic:0.41--hdfd78af_0
  - command: vdb-config
    docker_image: quay.io/biocontainers/sra-tools:3.4.1--h4304569_1
    docker_command: vdb-config
  - command: vep
    docker_image: quay.io/biocontainers/ensembl-vep:116.2--pl5321h2a3209d_0
    docker_command: vep
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:482--hdc0a859_1
    docker_args: -i