Mercurial > repos > immuneml > immuneml_tools

annotate README.md @ 3:ed3932e6d616 draft

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"planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
author immuneml
date Thu, 01 Jul 2021 16:51:28 +0000
parents 629e7e403e19
children 48569213d91c
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1 # immuneml_tools
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2 Galaxy tool wrappers for immuneML.
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3 https://immuneml.uio.no/
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5 ## Installation:
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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.
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8 ### New datatype `immuneml_receptors`
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9 No matter how you install the tools, you will need to define a new datatype, which is done as follows:
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11 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set
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12 ```
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13 datatypes_config_file: datatypes_conf.xml
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14 ```
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15 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
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16 3. Add the following line to your `datatypes_config_file`:
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17 ```
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18 <datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>
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19 ```
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20 The line has to be inside `<registration>` along with the other datatypes.
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22 ### The immuneML conda package
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23 Galaxy will need to install the immuneML conda package. This conda installation typically takes several minutes.