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# immuneml_tools
Galaxy tool wrappers for immuneML.
https://immuneml.uio.no/

## Installation:
The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way.

### New datatype `iml_dataset`
No matter how you install the tools, you will need to define a new datatype, which is done as follows:

1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set
```
datatypes_config_file: datatypes_conf.xml
```
2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
3. Add the following line to your `datatypes_config_file`:
```
<datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/>
```
The line has to be inside `<registration>` along with the other datatypes.

### The immuneML conda package
Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes.