Mercurial > repos > immuneml > immuneml_tools

annotate README.rst @ 15:e33b3d370124 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 5d2abc4e7c3895a90cefc6384e0964049e9bcb9f"
author immuneml
date Tue, 04 Jan 2022 12:57:42 +0000
parents 2d3dd9ff7e84
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
1 The tools rely on immuneML version 2.0.1 or newer.
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
2
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
3 Installation
1
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
4 ============
3
ed3932e6d616 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents: 2
diff changeset
5 You will need to define a new datatype ``immuneml_receptors``, which is done as follows:
1
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
6
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
7 1. In your ``galaxy.yml`` look up the name of your ``datatypes_config_file``. If the name is not yet defined, set
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
8
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
9 ``datatypes_config_file: datatypes_conf.xml``
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
10
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
11 2. Make ``datatypes_conf.xml`` by copying ``datatypes_conf.xml.sample`` unless a ``datatypes_config_file`` was already defined.
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
12 3. Add the following line to your ``datatypes_config_file``:
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
13
3
ed3932e6d616 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents: 2
diff changeset
14 ``<datatype extension="immuneml_receptors" type="galaxy.datatypes.text:Html" subclass="True"/>``
1
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
15 The line has to be inside ``<registration>`` along with the other datatypes.
08042588bd02 "planemo upload commit 2fed2858d4044a3897a93a5604223d1d183ceac0-dirty"
immuneml
parents:
diff changeset
16
6
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
17 The immuneML package
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
18 ====================
2d3dd9ff7e84 "planemo upload commit 74f2bd15d2b7723c8e5a22d743913706dc7d8333-dirty"
immuneml
parents: 5
diff changeset
19 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