This repo contains build instructions that we use at the Center for Data-Driven Discovery in Biomedicine (D3B) and in the Kids First Data Resource Center (KFDRC). The most updated production images are stored in the SBG docker registry. This requires a Cavatica login and individual images may require separate permission to access.
Legacy versions of some images are stored in the KFDRC Dockerhub. The images on Dockerhub are deprecated and will not be updated.
Below is a list of the current docker images the command to pull them.
| image | version | pull command |
|---|---|---|
| BIC-seq2 | 0.7.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/BIC-seq2:0.7.2 |
| FusionCatcher | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/FusionCatcher:latest |
| LinkedSV | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/LinkedSV:latest |
| SVTyper | 0.7.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/SVTyper:0.7.1 |
| THetA2 | 0.7.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/THetA2:0.7.0 |
| THetA2 | 0.7.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/THetA2:0.7.1 |
| VEP | r93.7 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VEP:r93.7 |
| VEP | r93 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VEP:r93 |
| VEP | r93_v2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VEP:r93_v2 |
| VEP | r94 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VEP:r94 |
| VEP | r98 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VEP:r98 |
| VarDictJava | 1.5.8 | docker pull pgc-images.sbgenomics.com/d3b-bixu/VarDictJava:1.5.8 |
| VarDictJava | fp_filter | docker pull pgc-images.sbgenomics.com/d3b-bixu/VarDictJava:fp_filter |
| add-strelka2-fields | 1.0.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/add-strelka2-fields:1.0.0 |
| annoFuse | 0.1.8 | docker pull pgc-images.sbgenomics.com/d3b-bixu/annoFuse:0.1.8 |
| annoFuse | 0.90.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/annoFuse:0.90.0 |
| annovar | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/annovar:latest |
| arriba | 1.0.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/arriba:1.0.1 |
| arriba | 1.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/arriba:1.1.0 |
| arriba | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/arriba:latest |
| bcbio | variation_recall-0.2.4 | docker pull pgc-images.sbgenomics.com/d3b-bixu/bcbio:variation_recall-0.2.4 |
| bed_tools | bedopsv2.4.36_plus_bedtools | docker pull pgc-images.sbgenomics.com/d3b-bixu/bed_tools:bedopsv2.4.36_plus_bedtools |
| bwa-bundle | 0.1.17 | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa-bundle:0.1.17 |
| bwa-picard | broad | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa-picard:broad |
| bwa-picard | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa-picard:latest |
| bwa | 0.7.15-r1140 | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:0.7.15-r1140 |
| bwa | 0.7.17-r1188 | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:0.7.17-r1188 |
| bwa | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa:latest |
| canvas | 1.11.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/canvas:1.11.0 |
| cellranger | 3.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:3.1 |
| cellranger | 5.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:5.0 |
| cellranger | 6.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:6.0 |
| cnvnator | v0.4.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/cnvnator:v0.4.1 |
| codex2 | 3.8 | docker pull pgc-images.sbgenomics.com/d3b-bixu/codex2:3.8 |
| consensus-merge | 1.0.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/consensus-merge:1.0.0 |
| consensus-merge | 1.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/consensus-merge:1.1.0 |
| controlfreec | 11.5 | docker pull pgc-images.sbgenomics.com/d3b-bixu/controlfreec:11.5 |
| cutadapt | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/cutadapt:latest |
| fastqc | v0.11.9 | docker pull pgc-images.sbgenomics.com/d3b-bixu/fastqc:v0.11.9 |
| freebayes | v1.3.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/freebayes:v1.3.1 |
| freebayes | v1.3.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/freebayes:v1.3.2 |
| gatk-picard | 4.0.1.2-2.8.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk-picard:4.0.1.2-2.8.3 |
| gatk-picard | 4.beta.1-2.8.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk-picard:4.beta.1-2.8.3 |
| gatk | 3.5-0-g36282e4 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:3.5-0-g36282e4 |
| gatk | 3.6-0-g89b7209 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:3.6-0-g89b7209 |
| gatk | 3.8 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:3.8 |
| gatk | 3.8_ubuntu | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:3.8_ubuntu |
| gatk | 4.0.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.0.1.0 |
| gatk | 4.0.1.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.0.1.2 |
| gatk | 4.0.12.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.0.12.0 |
| gatk | 4.0.5.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.0.5.2 |
| gatk | 4.1.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.1.1.0 |
| gatk | 4.1.7.0R | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.1.7.0R |
| gatk | 4.2.0.0R | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.2.0.0R |
| gatk | 4.beta.1-3.5 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.1-3.5 |
| gatk | 4.beta.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.1 |
| gatk | 4.beta.5-tabix | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.5-tabix |
| gatk | 4.beta.5 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.5 |
| gatk | 4.beta.6-tabix | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6-tabix |
| gatk | 4.beta.6 | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6 |
| gatk | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:latest |
| hotspots | 0.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/hotspots:0.1.0 |
| kf_vcf2maf | v1.0.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/kf_vcf2maf:v1.0.0 |
| kf_vcf2maf | v1.0.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/kf_vcf2maf:v1.0.1 |
| kf_vcf2maf | v1.0.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/kf_vcf2maf:v1.0.2 |
| kf_vcf2maf | v1.0.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/kf_vcf2maf:v1.0.3 |
| lancet | 1.0.7 | docker pull pgc-images.sbgenomics.com/d3b-bixu/lancet:1.0.7 |
| loompy | 2.0.16 | docker pull pgc-images.sbgenomics.com/d3b-bixu/loompy:2.0.16 |
| lumpy-sv | 0.2.13 | docker pull pgc-images.sbgenomics.com/d3b-bixu/lumpy-sv:0.2.13 |
| lumpy-sv | 0.3.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/lumpy-sv:0.3.0 |
| manta | 1.4 | docker pull pgc-images.sbgenomics.com/d3b-bixu/manta:1.4 |
| manta | 1.6.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/manta:1.6.0 |
| peddy | v0.4.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/peddy:v0.4.2 |
| peddy | v0.4.7 | docker pull pgc-images.sbgenomics.com/d3b-bixu/peddy:v0.4.7 |
| picard-r | picard2.15.0-r.3.3.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard-r:picard2.15.0-r.3.3.3 |
| picard-r | picard2.8.3-r3.3.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard-r:picard2.8.3-r3.3.3 |
| picard | 2.14.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.14.0 |
| picard | 2.15.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.15.0 |
| picard | 2.17.4 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.17.4 |
| picard | 2.18.9 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9 |
| picard | 2.18.9R | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.18.9R |
| picard | 2.8.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:2.8.3 |
| picard | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/picard:latest |
| pizzly | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/pizzly:latest |
| python | 2.7.13 | docker pull pgc-images.sbgenomics.com/d3b-bixu/python:2.7.13 |
| sambamba | 0.6.3 | docker pull pgc-images.sbgenomics.com/d3b-bixu/sambamba:0.6.3 |
| sambamba | 0.7.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/sambamba:0.7.1 |
| samtools | 1.3.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.3.1 |
| samtools | 1.6 | docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.6 |
| samtools | 1.7-11-g041220d | docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.7-11-g041220d |
| samtools | 1.9 | docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.9 |
| samtools | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:latest |
| seurat | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/seurat:latest |
| smoove | 0.2.5 | docker pull pgc-images.sbgenomics.com/d3b-bixu/smoove:0.2.5 |
| soupx_R | 4.1.0_SoupX | docker pull pgc-images.sbgenomics.com/d3b-bixu/soupx_R:4.1.0_SoupX |
| speedseq | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/speedseq:latest |
| star | 2.6.1d | docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.6.1d |
| star | 2.7.5a | docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.7.5a |
| star | fusion-1.5.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/star:fusion-1.5.0 |
| strelka | v2.9.10 | docker pull pgc-images.sbgenomics.com/d3b-bixu/strelka:v2.9.10 |
| sv2 | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/sv2:latest |
| svaba | 1.1.0 | docker pull pgc-images.sbgenomics.com/d3b-bixu/svaba:1.1.0 |
| velocyto | 0.17.17 | docker pull pgc-images.sbgenomics.com/d3b-bixu/velocyto:0.17.17 |
| verifybamid | 1.0.1 | docker pull pgc-images.sbgenomics.com/d3b-bixu/verifybamid:1.0.1 |
| verifybamid | 1.0.2 | docker pull pgc-images.sbgenomics.com/d3b-bixu/verifybamid:1.0.2 |
| verifybamid | latest | docker pull pgc-images.sbgenomics.com/d3b-bixu/verifybamid:latest |
| zumis | 2.9.4 | docker pull pgc-images.sbgenomics.com/d3b-bixu/zumis:2.9.4 |