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Make docker #2

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212fc8f
ENH: fixed the reaction parsing from metanetx
Oct 2, 2025
c3c7f14
ENH: switched the taxonomy id to be at a lower levek
Oct 13, 2025
5a63efd
ENH: working nextflow workflows
Oct 14, 2025
bd4131b
ENH: the pubchem search includes xref and lowest CID based on int for…
Oct 15, 2025
1484d42
ENH: added pubchem xref search
Oct 18, 2025
e02408f
ENH: still working on it
Nov 11, 2025
436eb95
ENH: small changes
Dec 4, 2025
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13 changes: 13 additions & 0 deletions README.md
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Expand Up @@ -43,6 +43,12 @@ Pulls the image directly from Docker Hub:
docker compose --profile hub up --build
```

Or build directly:

```bash
docker build -t biopathopt:latest -f images/Dockerfile.original .
```

### 2. Build from `images/Dockerfile.cache`

Uses the cached build recipe for faster local builds. This is because the repeated
Expand All @@ -53,6 +59,7 @@ following file to generate the cache before :
docker compose --profile cache up --build
```


### 3. Build from `images/Dockerfile` with `BRENDA_FILE`

Allows you to specify which **Brenda flatfile** to include at build time. Note
Expand All @@ -68,6 +75,12 @@ docker compose --profile full up --build
BRENDA_FILE=brenda_2025_1.json docker compose --profile full up --build
```

Or build directly:

```bash
docker build -t biopathopt:cache -f images/Dockerfile.cache .
```

### Notes

- The JupyterLab server will be available at **http://localhost:8085**.
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