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D3B Docker Image Build Instruction Hub

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.

Current Dockers

Last Monthly Build

Last Monthly Pull

Below is a list of the current docker images the command to pull them.

image version pull command
add-strelka2-fields 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/add-strelka2-fields:1.0.0
annoFuse 0.90.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/annofuse:0.90.0
annoFuse 0.91.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/annofuse:0.91.0
annoFuse 0.92.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/annofuse:0.92.0
annotsv 3.1.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/annotsv:3.1.1
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 2.2.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/arriba:2.2.1
arriba latest docker pull pgc-images.sbgenomics.com/d3b-bixu/arriba:latest
autopvs1 v1.0.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v1.0.1
autopvs1 v2.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/autopvs1:v2.0.0
bcbio variation_recall-0.2.4 docker pull pgc-images.sbgenomics.com/d3b-bixu/bcbio:variation_recall-0.2.4
bcftools 1.20 docker pull pgc-images.sbgenomics.com/d3b-bixu/bcftools:1.20
bed_tools bedopsv2.4.36_plus_bedtools docker pull pgc-images.sbgenomics.com/d3b-bixu/bed_tools:bedopsv2.4.36_plus_bedtools
BIC-seq2 0.7.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/bic-seq2:0.7.2
bvcftools latest docker pull pgc-images.sbgenomics.com/d3b-bixu/bvcftools:latest
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-samtools latest docker pull pgc-images.sbgenomics.com/d3b-bixu/bwa-samtools: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
cellranger 6.1.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/cellranger:6.1.2
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 3.4 docker pull pgc-images.sbgenomics.com/d3b-bixu/cutadapt:3.4
cutadapt latest docker pull pgc-images.sbgenomics.com/d3b-bixu/cutadapt:latest
cutesv 1.0.13 docker pull pgc-images.sbgenomics.com/d3b-bixu/cutesv:1.0.13
cutesv 2.0.3 docker pull pgc-images.sbgenomics.com/d3b-bixu/cutesv:2.0.3
echtvar 0.1.9 docker pull pgc-images.sbgenomics.com/d3b-bixu/echtvar:0.1.9
echtvar 0.2.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/echtvar:0.2.0
echtvar 0.2.0-rc docker pull pgc-images.sbgenomics.com/d3b-bixu/echtvar:0.2.0-rc
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
FusionAnnotator 0.1.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/fusionannotator:0.1.1
FusionCatcher latest docker pull pgc-images.sbgenomics.com/d3b-bixu/fusioncatcher:latest
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 docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.1
gatk 4.beta.1-3.5 docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.1-3.5
gatk 4.beta.5 docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.5
gatk 4.beta.5-tabix docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.5-tabix
gatk 4.beta.6 docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6
gatk 4.beta.6-tabix docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:4.beta.6-tabix
gatk latest docker pull pgc-images.sbgenomics.com/d3b-bixu/gatk:latest
gistic latest docker pull pgc-images.sbgenomics.com/d3b-bixu/gistic:latest
hbc_scrna_qc scrnaseq docker pull pgc-images.sbgenomics.com/d3b-bixu/hbc_scrna_qc:scrnaseq
hisat2 2.2.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/hisat2:2.2.1
hotspots 0.1.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/hotspots:0.1.0
intervar v2.2.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/intervar:v2.2.1
isoseq v4.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/isoseq:v4.0.0
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
lancet 1.1.x docker pull pgc-images.sbgenomics.com/d3b-bixu/lancet:1.1.x
lima v2.9.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/lima:v2.9.0
LinkedSV latest docker pull pgc-images.sbgenomics.com/d3b-bixu/linkedsv:latest
LOH 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/loh:1.0.0
LOH 1.0.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/loh:1.0.1
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
mend_qc latest docker pull pgc-images.sbgenomics.com/d3b-bixu/mend_qc:latest
minimap2 v2.28 docker pull pgc-images.sbgenomics.com/d3b-bixu/minimap2:v2.28
msisensor 1.1.a docker pull pgc-images.sbgenomics.com/d3b-bixu/msisensor:1.1.a
nanocount v1.1.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/nanocount:v1.1.0
ngscheckmate 1.3 docker pull pgc-images.sbgenomics.com/d3b-bixu/ngscheckmate:1.3
octopus 0.6.3-beta docker pull pgc-images.sbgenomics.com/d3b-bixu/octopus:0.6.3-beta
pbfusion v0.4.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/pbfusion:v0.4.1
pbta-splicing 0.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/pbta-splicing:0.1
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
phlat 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/phlat:1.0.0
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
pigeon v1.2.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/pigeon:v1.2.0
pizzly latest docker pull pgc-images.sbgenomics.com/d3b-bixu/pizzly:latest
plink 1.90b7.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/plink:1.90b7.2
PureCN latest docker pull pgc-images.sbgenomics.com/d3b-bixu/purecn:latest
pypy 3 docker pull pgc-images.sbgenomics.com/d3b-bixu/pypy:3
pyspark 3.1.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/pyspark:3.1.2
python 2.7.13 docker pull pgc-images.sbgenomics.com/d3b-bixu/python:2.7.13
python 3.9-canine-util docker pull pgc-images.sbgenomics.com/d3b-bixu/python:3.9-canine-util
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 1.15.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.15.1
samtools 1.20-parallel docker pull pgc-images.sbgenomics.com/d3b-bixu/samtools:1.20-parallel
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
sanger caveman-pindel docker pull pgc-images.sbgenomics.com/d3b-bixu/sanger:caveman-pindel
scdblfinder 1.8.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/scdblfinder:1.8.0
scdblfinder v1.12.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/scdblfinder:v1.12.0
scRNA_qc v1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/scrna_qc:v1.0.0
scRNA_qc v1.0.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/scrna_qc:v1.0.1
scRNA_qc v1.1.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/scrna_qc:v1.1.0
scrublet 0.2.3 docker pull pgc-images.sbgenomics.com/d3b-bixu/scrublet:0.2.3
sentieon 202112.01_hifi docker pull pgc-images.sbgenomics.com/d3b-bixu/sentieon:202112.01_hifi
seqkit 2.3.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/seqkit:2.3.1
sequenza 3.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/sequenza:3.0.0
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
sniffles 2.0.3 docker pull pgc-images.sbgenomics.com/d3b-bixu/sniffles:2.0.3
sniffles 2.0.7 docker pull pgc-images.sbgenomics.com/d3b-bixu/sniffles:2.0.7
snpEff 4.3t docker pull pgc-images.sbgenomics.com/d3b-bixu/snpeff:4.3t
snpEff latest docker pull pgc-images.sbgenomics.com/d3b-bixu/snpeff:latest
soupx_R 1.6.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/soupx_r:1.6.2
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 2.7.10a docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.7.10a
star 2.7.10b docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.7.10b
star 2.7.11a docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.7.11a
star 2.7.5a docker pull pgc-images.sbgenomics.com/d3b-bixu/star:2.7.5a
star fusion-1.10.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/star:fusion-1.10.1
star fusion-1.5.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/star:fusion-1.5.0
stranded 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/stranded:1.0.0
stranded 1.1.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/stranded:1.1.0
strelka v2.9.10 docker pull pgc-images.sbgenomics.com/d3b-bixu/strelka:v2.9.10
supremo 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/supremo:1.0.0
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
SVTyper 0.7.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/svtyper:0.7.1
t1k v1.0.2 docker pull pgc-images.sbgenomics.com/d3b-bixu/t1k:v1.0.2
t1k v1.0.5 docker pull pgc-images.sbgenomics.com/d3b-bixu/t1k:v1.0.5
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
tidyverse 3.6.1-canine-util docker pull pgc-images.sbgenomics.com/d3b-bixu/tidyverse:3.6.1-canine-util
toolkit_immune_deconvolution 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_immune_deconvolution:1.0.0
toolkit_subtyping 4.1.0R docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_subtyping:4.1.0R
toolkit_subtyping pyreader0.4.4 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_subtyping:pyreader0.4.4
toolkit_subtyping subtyping_v1.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_subtyping:subtyping_v1.0
toolkit_subtyping subtyping_v1.1 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_subtyping:subtyping_v1.1
toolkit_subtyping subtyping_v2.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_subtyping:subtyping_v2.0
toolkit_tmb 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/toolkit_tmb:1.0.0
tumor-only-benchmarking 1.0.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/tumor-only-benchmarking:1.0.0
VarDictJava 1.5.8 docker pull pgc-images.sbgenomics.com/d3b-bixu/vardictjava:1.5.8
VarDictJava 1.7.0 docker pull pgc-images.sbgenomics.com/d3b-bixu/vardictjava:1.7.0
VarDictJava fp_filter docker pull pgc-images.sbgenomics.com/d3b-bixu/vardictjava:fp_filter
vcf_utils latest docker pull pgc-images.sbgenomics.com/d3b-bixu/vcf_utils:latest
velocyto 0.17.17 docker pull pgc-images.sbgenomics.com/d3b-bixu/velocyto:0.17.17
VEP r93 docker pull pgc-images.sbgenomics.com/d3b-bixu/vep:r93
VEP r93.7 docker pull pgc-images.sbgenomics.com/d3b-bixu/vep:r93.7
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
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
WGSA latest docker pull pgc-images.sbgenomics.com/d3b-bixu/wgsa:latest
zumis 2.9.4 docker pull pgc-images.sbgenomics.com/d3b-bixu/zumis:2.9.4

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bixtools's Issues

Publish images to github

Now that GitHub offers package repositories for docker images, it would be nice if we could add some CI work to publish these packages to it upon merges to master.

Fix status checks

It would appear that the dockercloud status check has been failing for some time.
We should ensure that all CI checks are passing and heeded. If the check is no longer valid, perhaps it should be removed.

Tag dockerfiles with consistent labels

All dockerfiles should have consistent formatting of their labels. This includes ensuring that all now deprecated MAINTAINER fields have been changed to labels.

At a bare minimum, images should have the following labels:

LABEL maintainer="[email protected]"

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