annotate README.md @ 19:051d349fdc8c draft default tip

"planemo upload commit 5ffe9db26c26d30c923c812b69346d95948e9cd0"
author immuneml
date Tue, 05 Apr 2022 10:11:52 +0000
parents 2d3dd9ff7e84
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
1 # immuneml_tools
5
48569213d91c "planemo upload commit 49b58953ab7eec02a6917044be672ad9a65eab5c-dirty"
immuneml
parents: 3
diff changeset
2 Galaxy tool wrappers for immuneML. The tools rely on immuneML version 2.0.1 or newer.
48569213d91c "planemo upload commit 49b58953ab7eec02a6917044be672ad9a65eab5c-dirty"
immuneml
parents: 3
diff changeset
3
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
4 https://immuneml.uio.no/
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
5
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
6 ## Installation:
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
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.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
8
3
ed3932e6d616 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents: 0
diff changeset
9 ### New datatype `immuneml_receptors`
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
10 No matter how you install the tools, you will need to define a new datatype, which is done as follows:
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
11
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
12 1. In your `galaxy.yml` look up the name of your `datatypes_config_file`. If the name is not yet defined, set
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
13 ```
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
14 datatypes_config_file: datatypes_conf.xml
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
15 ```
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
16 2. Make `datatypes_conf.xml` by copying `datatypes_conf.xml.sample` unless a `datatypes_config_file` was already defined.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
17 3. Add the following line to your `datatypes_config_file`:
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
18 ```
3
ed3932e6d616 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents: 0
diff changeset
19 <datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>
0
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
20 ```
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
21 The line has to be inside `<registration>` along with the other datatypes.
629e7e403e19 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
22
5
48569213d91c "planemo upload commit 49b58953ab7eec02a6917044be672ad9a65eab5c-dirty"
immuneml
parents: 3
diff changeset
23 ### The immuneML package
6
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
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
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
25