diff --git a/bulker/biobase.yaml b/bulker/biobase.yaml index 4e72f43..13452d3 120000 --- a/bulker/biobase.yaml +++ b/bulker/biobase.yaml @@ -1 +1 @@ -biobase_0.1.17.yaml \ No newline at end of file +biobase_0.1.18.yaml \ No newline at end of file diff --git a/bulker/biobase_0.1.18.yaml b/bulker/biobase_0.1.18.yaml new file mode 100644 index 0000000..b8f4940 --- /dev/null +++ b/bulker/biobase_0.1.18.yaml @@ -0,0 +1,181 @@ +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