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Add Scramble docker to the build script & update docs (#608)
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* Add scramble to build_docker.py.

* Update docs to include the Scramble docker image.

* Manta docker image is now based on the ubuntu 22.04 image.
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@VJalili
VJalili authored Oct 16, 2023
1 parent 893abd9 commit 8bcdb15
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3 changes: 3 additions & 0 deletions scripts/docker/build_docker.py
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Expand Up @@ -176,6 +176,9 @@ class to track dependencies, control build and push of entire job
docker_dependencies={
"sv-base": "SVBASE_IMAGE"}
),
"scramble": ImageDependencies(
git_dependencies=("dockerfiles/scramble/*")
),
"wham": ImageDependencies(
git_dependencies="dockerfiles/wham/*",
docker_dependencies={
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6 changes: 4 additions & 2 deletions website/docs/advanced/docker/images.md
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Expand Up @@ -29,7 +29,7 @@ The figure below illustrates the relationships between the GATK-SV Docker images

```mermaid
flowchart TD
ubuntu22[Ubuntu 22.04] --> svbasemini[sv-base-mini] & samtoolsenv[samtools-cloud-virtual-env] & svbaseenv[sv-base-virtual-env]
ubuntu2204[Ubuntu 22.04] --> svbasemini[sv-base-mini] & samtoolsenv[samtools-cloud-virtual-env] & svbaseenv[sv-base-virtual-env]
svbasemini & samtoolsenv & svbaseenv --> svpipelineenv[sv-pipeline-virtual-env]
samtoolsenv --> samtoolscloud[samtools-cloud] & svutilsenv[sv-utils-env]
svbasemini --> samtoolscloud
Expand All @@ -39,9 +39,10 @@ flowchart TD
svbaseenv --> cnmopsenv[cnmpos-virtual-env]
svbase & cnmopsenv --> cnmpos[cnmops]
ubuntu18[Ubuntu 18.04] --> manta[Manta] & melt[MELT] & wham[Wham]
ubuntu1804[Ubuntu 18.04] --> melt[MELT] & wham[Wham]
samtoolscloud --> wham
ubuntu2210[Ubuntu 22.10] --> str[STR]
ubuntu2204 --> scramble[Scramble] & manta[Manta]
```

The image depicts the hierarchical relationship among GATK-SV
Expand All @@ -66,6 +67,7 @@ The table below lists the GATK-SV Docker images and their dependencies.
|------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------|
| `manta` | <ul><li>`dockerfiles/manta/*`</li></ul> | |
| `melt` | <ul><li>`dockerfiles/melt/*`</li></ul> | <ul><li>`sv-base`</li></ul> |
| `scramble` | <ul><li>`dockerfiles/scramble/*`</li></ul> | |
| `wham` | <ul><li>`dockerfiles/wham/*`</li></ul> | <ul><li>`samtools-cloud`</li></ul> |
| `str` | <ul><li>`dockerfiles/str/*`</li></ul> | |
| `sv-base-mini` | <ul><li>`dockerfiles/sv-base-mini/*`</li></ul> | |
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6 changes: 3 additions & 3 deletions website/package.json
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Expand Up @@ -14,9 +14,9 @@
"write-heading-ids": "docusaurus write-heading-ids"
},
"dependencies": {
"@docusaurus/core": "2.4.1",
"@docusaurus/preset-classic": "2.4.1",
"@docusaurus/theme-mermaid": "^2.4.1",
"@docusaurus/core": "2.4.3",
"@docusaurus/preset-classic": "2.4.3",
"@docusaurus/theme-mermaid": "^2.4.3",
"@mdx-js/react": "^1.6.22",
"clsx": "^1.2.1",
"prism-react-renderer": "^1.3.5",
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