comparison README.md @ 0:18a8d140ec6f draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f

0:18a8d140ec6f

## Tool versions

Dorado is distributed on
[DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech.
The containers are identified by sha256 hash, but not tagged with a version.

We can still use the containers and display the dorado version by hard-coding
both dorado version and container hash into the wrapper (see `macros.xml`).
Unfortunately you have to pull a >6 GB container and run `dorado --version` just
to check the tool version. This also prevents auto-updates of this wrapper.

You can update the list of models at the same time (see
below). **You must do this when you update the wrapper**.

## Basecalling models

The models are bundled in the container at `/models` and made available by the
`dorado_models.loc` file. 

The columns are `value`, `container_hash`, `name` and  `path`.

To update the list, modify `tool-data/dorado_models.loc.sample`.

Because models can be added and removed, models are listed **per container** in
the loc file.

Here's some code to **append** the models from the container with hash
`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`  to the loc file.

```bash
export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28"

apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \
    ls /models | \
    awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \
    >> tool-data/dorado_models.loc.sample
```

The loc file doesn't have a header, so you can keep it sorted.

```bash
cp tool-data/dorado_models.loc.sample \
    tool-data/dorado_models.loc.sample.old &&
sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \
    > tool-data/dorado_models.loc
```