bulker/biobase:0.0.8

Raw Manifest

manifest:
  name: bulker/biobase
  version: 0.0.8
  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: aws
    docker_image: mesosphere/aws-cli
  - command: bamtools
    docker_image: quay.io/biocontainers/bamtools:2.5.1--he860b03_5
  - command: bedClip
    docker_image: quay.io/biocontainers/ucsc-bedclip:377--h446ed27_1
    docker_args: -i
  - command: bedCommonRegions
    docker_image: quay.io/biocontainers/ucsc-bedcommonregions:377--h446ed27_1
    docker_args: -i
  - command: bedGraphToBigWig
    docker_image: quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1
    docker_args: -i
  - command: bedIntersect
    docker_image: quay.io/biocontainers/ucsc-bedintersect:377--h446ed27_1
    docker_args: -i
  - command: bedItemOverlapCount
    docker_image: quay.io/biocontainers/ucsc-beditemoverlapcount:377--h446ed27_1
    docker_args: -i
  - command: bedops
    docker_image: quay.io/biocontainers/bedops:2.4.39--hc9558a2_0
  - command: bedPileUps
    docker_image: quay.io/biocontainers/ucsc-bedpileups:377--h446ed27_1
    docker_args: -i
  - command: bedToBigBed
    docker_image: quay.io/biocontainers/ucsc-bedtobigbed:377--h446ed27_1
    docker_args: -i
  - command: bedtools
    docker_image: quay.io/biocontainers/bedtools:2.29.0--hc088bd4_3
    docker_args: -i
  - command: bigBedToBed
    docker_image: quay.io/biocontainers/ucsc-bigbedtobed:377--h446ed27_1
    docker_args: -i
  - command: bigWigAverageOverBed
    docker_image: quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h446ed27_1
    docker_args: -i
  - command: bigWigCat
    docker_image: quay.io/biocontainers/ucsc-bigwigcat:377--h446ed27_1
    docker_args: -i
  - command: bigWigSummary
    docker_image: quay.io/biocontainers/ucsc-bigwigsummary:377--h446ed27_1
    docker_args: -i
  - command: bigWigToWig
    docker_image: quay.io/biocontainers/ucsc-bigwigtowig:377--h446ed27_1
    docker_args: -i
  - command: bismark
    docker_image: quay.io/biocontainers/bismark:0.22.3--0
  - command: bissnp
    docker_image: quay.io/biocontainers/bis-snp:1.0.1--2
  - command: blast
    docker_image: quay.io/biocontainers/blast:2.9.0--pl526he19e7b1_5
  - command: bowtie
    docker_image: quay.io/biocontainers/bowtie:1.2.3--py37hc9558a2_0
  - command: bowtie2
    docker_image: quay.io/biocontainers/bowtie2:2.4.1--py37h4ef193e_2
  - command: bsmap
    docker_image: quay.io/biocontainers/bsmap:2.90--he860b03_2
  - command: bwa
    docker_image: quay.io/biocontainers/bwa:0.7.17--hed695b0_7
  - command: cellranger
    docker_image: quay.io/xujishu/cellranger:3.1.0
  - command: cufflinks
    docker_image: quay.io/biocontainers/cufflinks:2.2.1--py36_2
  - command: curl
    docker_image: curlimages/curl:7.69.1
    docker_command: curl
    docker_args: -i
  - command: cutadapt
    docker_image: quay.io/biocontainers/cutadapt:2.10--py37h516909a_0
  - command: faSplit
    docker_image: quay.io/biocontainers/ucsc-fasplit:377--h446ed27_1
  - command: fasterq-dump
    docker_image: quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3
    docker_command: fasterq-dump
  - command: fastq-dump
    docker_image: quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3
    docker_command: fastq-dump
  - command: fastqc
    docker_image: quay.io/biocontainers/fastqc:0.11.8--1
  - command: gatk
    docker_image: broadinstitute/gatk:4.1.7.0
    docker_command: gatk
  - command: gt
    docker_image: quay.io/biocontainers/genometools-genometools:1.5.10--py37h997e34b_3
  - command: hisat2
    docker_image: quay.io/biocontainers/hisat2:2.2.0--py37h3340039_3
  - command: homer
    docker_image: quay.io/biocontainers/homer:4.11--pl526h99015e2_1
  - command: kallisto
    docker_image: quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1
  - command: khmer
    docker_image: quay.io/biocontainers/khmer:3.0.0a3--py37hf484d3e_0
  - command: liftOver
    docker_image: quay.io/biocontainers/ucsc-liftover:482--h0b57e2e_0
  - command: macs2
    docker_image: quay.io/biocontainers/macs2:2.2.6--py37h516909a_0
  - command: mashmap
    docker_image: quay.io/biocontainers/mashmap:2.0--h9dd4a16_2
  - command: multiqc
    docker_image: quay.io/biocontainers/multiqc:1.13a--pyhdfd78af_1
  - command: picard
    docker_image: broadinstitute/picard:2.22.3
    docker_command: picard
  - command: pigz
    docker_image: nsheff/pigz
    docker_command: pigz
    docker_args: -i
  - command: prefetch
    docker_image: quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3
    docker_command: prefetch
  - command: R
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_11
    docker_command: R
    docker_args: -it
    description: You should add --volume=${HOME}/R/4.0:/usr/local/lib/R/host-site-library
      to tool_args
  - command: refgenie
    docker_image: databio/refgenie
  - command: repeatmasker
    docker_image: quay.io/biocontainers/repeatmasker:4.0.9_p2--pl526_2
  - command: rg
    docker_image: peccu/rg
  - command: Rscript
    docker_image: bioconductor/bioconductor_docker:RELEASE_3_11
    docker_command: Rscript
    docker_args: -it
  - command: salmon
    docker_image: quay.io/biocontainers/salmon:1.2.1--hf69c8f4_0
  - command: sambamba
    docker_image: quay.io/biocontainers/sambamba:0.7.1--h148d290_0
  - command: samblaster
    docker_image: quay.io/biocontainers/samblaster:0.1.26--hc9558a2_0
  - command: samtools
    docker_args: -i
    docker_image: quay.io/biocontainers/samtools:1.10--h9402c20_2
  - command: segway
    docker_image: quay.io/biocontainers/segway:3.0--py_0
  - command: seqkit
    docker_image: quay.io/biocontainers/seqkit:0.10.2--0
  - command: seqtk
    docker_args: -i
    docker_image: quay.io/biocontainers/seqtk:1.3--hed695b0_2
  - command: skewer
    docker_image: quay.io/biocontainers/skewer:0.2.2--h2d50403_2
  - command: STAR
    docker_image: quay.io/biocontainers/star:2.7.3a--0
  - command: tabix
    docker_image: quay.io/biocontainers/htslib:1.6--0
  - 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
  - command: vdb-config
    docker_image: quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3
    docker_command: vdb-config
  - command: vep
    docker_image: quay.io/biocontainers/ensembl-vep:94.5--pl526ha4d7672_0
    docker_command: vep
  - command: wigToBigWig
    docker_image: quay.io/biocontainers/ucsc-wigtobigwig:377--h446ed27_1
    docker_args: -i