-
Notifications
You must be signed in to change notification settings - Fork 9
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
8 changed files
with
103 additions
and
19 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
|
|
||
| ## Tool versions | ||
|
|
||
| Dorado is distributed on | ||
| [DockerHub](https://hub.docker.com/r/nanoporetech/dorado/tags) by nanoporetech, | ||
| but not tagged with a version. | ||
|
|
||
| That means the hash for the current version has to be hard-coded into the | ||
| wrapper. Unfortunately you have to pull a >6 GB container just to check the tool | ||
| version. At least you can update the list of models at the same time (see | ||
| below). | ||
|
|
||
| **Make sure you 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. To update the list, modify | ||
| `tool-data/dorado_models.loc.sample`. Note that if ONT remove models from the | ||
| container, doing this will also make them unavailable to Galaxy. Check the diff | ||
| before you merge. | ||
|
|
||
| Here's a one-liner to **replace** the contents of the loc file with the models that are bundled in the container `nanoporetech/dorado:shac2d8bc91ca2d043fed84d06cca92aaeb62bcc1cd`. | ||
|
|
||
| ```bash | ||
| apptainer exec docker://nanoporetech/dorado:shac2d8bc91ca2d043fed84d06cca92aaeb62bcc1cd \ | ||
| ls /models | \ | ||
| awk '{print $0 "\t" $0 "\t/models/" $0}' \ | ||
| > tool-data/dorado_models.loc.sample | ||
| ``` |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| <tool id="dorado" name="dorado" version="@CONTAINER_HASH@+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <tool id="dorado" name="dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
|
|
@@ -10,19 +10,16 @@ ln -s '$pod5_file' ./reads.pod5 && | |
| dorado basecaller | ||
| --emit-sam | ||
| ## TODO: get a list of models from /models (bundled with the container) | ||
| "/models/[email protected]" | ||
| '${model.fields.path}' | ||
| reads.pod5 | ||
| > output.sam | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="pod5_file" type="data" format="fast5" label="Raw fast5 file"/> | ||
| <!-- <param name="model" type="select"> | ||
| <options from_data_table="dorado_models" /> | ||
| </param> --> | ||
| <param name="index" type="select"> | ||
| <options from_data_table="bowtie_indexes" /> | ||
| <!-- TODO: the model needs to be linked to the tool version, e.g. to prevent trying to run a new model with a previous version of the tool. --> | ||
| <param name="model" type="select"> | ||
| <options from_data_table="dorado_models"/> | ||
| </param> | ||
| </inputs> | ||
| <outputs> | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| ../tool-data/dorado_models.loc.sample |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| <tables> | ||
| <!-- Locations of indexes in the Bowtie mapper format --> | ||
| <table name="bowtie_indexes" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="tool-data/bowtie_indices.loc" /> | ||
| <table name="dorado_models" comment_char="#"> | ||
| <columns>value, name, path</columns> | ||
| <file path="tool-data/dorado_models.loc" /> | ||
| </table> | ||
| </tables> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| <tables> | ||
| <!-- Locations of indexes in the Bowtie mapper format --> | ||
| <table name="bowtie_indexes" comment_char="#"> | ||
| <columns>value, dbkey, name, path</columns> | ||
| <file path="${__HERE__}/test-data/bowtie_indices.loc" /> | ||
| <table name="dorado_models" comment_char="#"> | ||
| <columns>value, name, path</columns> | ||
| <file path="${__HERE__}/test-data/dorado_models.loc" /> | ||
| </table> | ||
| </tables> |