Mercurial > repos > immuneml > immuneml_tools
comparison README.md @ 0:629e7e403e19 draft
"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
| author | immuneml |
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| date | Thu, 01 Jul 2021 11:36:43 +0000 |
| parents | |
| children | ed3932e6d616 |
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| 1 # immuneml_tools | |
| 2 Galaxy tool wrappers for immuneML. | |
| 3 https://immuneml.uio.no/ | |
| 4 | |
| 5 ## Installation: | |
| 6 The tools can be installed from a Galaxy toolshed. You can also install them offline by editing Galaxy config files in the usual way. | |
| 7 | |
| 8 ### New datatype `iml_dataset` | |
| 9 No matter how you install the tools, you will need to define a new datatype, which is done as follows: | |
| 10 | |
| 11 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set | |
| 12 ``` | |
| 13 datatypes_config_file: datatypes_conf.xml | |
| 14 ``` | |
| 15 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined. | |
| 16 3. Add the following line to your `datatypes_config_file`: | |
| 17 ``` | |
| 18 <datatype extension="iml_dataset" type="galaxy.datatypes.text:Html" subclass="True"/> | |
| 19 ``` | |
| 20 The line has to be inside `<registration>` along with the other datatypes. | |
| 21 | |
| 22 ### The immuneML conda package | |
| 23 Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes. |