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author galaxy-australia
date Tue, 15 Apr 2025 07:04:29 +0000
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2 ## Tool versions
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4 Dorado is distributed on
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5 [DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech.
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6 The containers are identified by sha256 hash, but not tagged with a version.
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8 We can still use the containers and display the dorado version by hard-coding
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9 both dorado version and container hash into the wrapper (see `macros.xml`).
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10 Unfortunately you have to pull a >6 GB container and run `dorado --version` just
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11 to check the tool version. This also prevents auto-updates of this wrapper.
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13 You can update the list of models at the same time (see
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14 below). **You must do this when you update the wrapper**.
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16 ## Basecalling models
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18 The models are bundled in the container at `/models` and made available by the
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19 `dorado_models.loc` file.
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21 The columns are `value`, `container_hash`, `name` and `path`.
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23 To update the list, modify `tool-data/dorado_models.loc.sample`.
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25 Because models can be added and removed, models are listed **per container** in
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26 the loc file.
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28 Here's some code to update the loc file with models from the container with hash
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29 `1c65eb070a9fc1d88710c4dc09b06541f96fdd28`.
0
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31 ```bash
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32 export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28"
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34 apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \
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35 ls /models | \
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36 awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \
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37 > tool-data/dorado_models.loc.sample
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38 ```
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40 The loc file doesn't have a header, so you can keep it sorted.
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42 ```bash
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43 cp tool-data/dorado_models.loc.sample \
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44 tool-data/dorado_models.loc.sample.old &&
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45 sort -t$'\t' -k1,1V tool-data/dorado_models.loc.sample.old \
2
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46 > tool-data/dorado_models.loc.sample
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47 ```
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48
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49 ## Kits and Barcodes
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51 The list of acceptable kits and barcodes is not specified in the Dorado
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52 documentation.
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54 A list of all sequencing kits is in [`kits.cpp`](https://github.com/nanoporetech/dorado/blob/master/dorado/models/kits.cpp)
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56 Parsed into XML with the following GNU Awk program:
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58 ```bash
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59 gawk '
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60 /namespace kit/ { in_kit_namespace = 1 }
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61 in_kit_namespace && /codes_map/ { in_map = 1; print "Entering kit::codes_map" }
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62 in_map && /^\s*\{/ {
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63 if (match($0, /\{\s*KC::[A-Z0-9_]+,\s*\{\s*"([^"]+)"/, m))
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64 print " <option value=\"" m[1] "\">" m[1] "</option>";
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65 }
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66 /^\s*};/ {
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67 if (in_map) {
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68 print "Exiting kit::codes_map";
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69 exit
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70 }
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71 }' kits.cpp
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72 ```
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73
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74 I believe the allowed barcodes are in [`barcode_kits.cpp`](https://github.com/nanoporetech/dorado/blob/master/dorado/utils/barcode_kits.cpp).
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76 Parsed into XML with the following GNU Awk program:
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78 ```bash
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79 gawk '
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80 /kit_info_map/ { in_map = 1 }
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81 in_map && /^\s*\{/ {
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82 if (match($0, /^\s*\{\s*"([^"]+)",/, m))
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83 print " <option value=\"" m[1] "\">" m[1] "</option>";
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84 }
5e67ea368004 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 4e9b34685eeea001562ec29e1f10f5ee2eeca19c
galaxy-australia
parents: 2
diff changeset
85 /^\s*};/ { if (in_map) exit }' barcode_kits.cpp
5e67ea368004 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 4e9b34685eeea001562ec29e1f10f5ee2eeca19c
galaxy-australia
parents: 2
diff changeset
86 ```