Mercurial > repos > immuneml > immuneml_tools

annotate README.md @ 9:d9a2f5b7448a draft

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"planemo upload commit 97c6b0b37098f81d2454174e7b8e50224270f25d-dirty"
author immuneml
date Fri, 30 Jul 2021 13:23:25 +0000
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1 # immuneml_tools
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2 Galaxy tool wrappers for immuneML. The tools rely on immuneML version 2.0.1 or newer.
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4 https://immuneml.uio.no/
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6 ## Installation:
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7 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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9 ### New datatype `immuneml_receptors`
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10 No matter how you install the tools, you will need to define a new datatype, which is done as follows:
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12 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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13 ```
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14 datatypes_config_file: datatypes_conf.xml
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15 ```
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16 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
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17 3. Add the following line to your `datatypes_config_file`:
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18 ```
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19 <datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>
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20 ```
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21 The line has to be inside `<registration>` along with the other datatypes.
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23 ### The immuneML package
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24 Conda installation of immuneML typically takes several minutes. There is general information about Galaxy dependency resolution here: https://docs.galaxyproject.org/en/release_20.05/admin/conda_faq.html
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