mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
1de2d73f38
This comes in two modes - simple lists of required attributes and per-attribute parameters that may specify defaults.
The following toy example:
```
<tool>
<expand macro="inputs" bar="hello" />
<macros>
<xml name="inputs" dollar_tokens="bar">
<inputs type="the type is $BAR$" />
</xml>
</macros>
</tool>
```
will evalute to ``<tool><inputs type="the type is hello" /><tool>``. The XML macro definition tag can now take in two new fixed attributes dollar_tokens and at_tokens - which will be interpreted as a list of parameter names. Each parameter can be specified when expanding the macros as simple attributes specifying the value of the parameter. The "dollar" parameter with name bar would map to a token with name $BAR$. Likewise an "at" parameter with name foo would map to a token with name @FOO@.
Both parameter types can be specified on a per-parameter basis to also specify default values. So the following example:
```
<tool>
<expand macro="inputs" foo="hello" />
<expand macro="inputs" foo="world" />
<expand macro="inputs" />
<macros>
<xml name="inputs" at_token_foo="the_default">
<inputs>@FOO@</inputs>
</xml>
</macros>
</tool>
```
Would evalute to ``<tool><inputs>hello</inputs><inputs>world</inputs><inputs>the_default</inputs>``.
Updated unit tests explain the above much more succinctly - though some like English and words for reasons that escape me.
.. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&target=galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy is available via `http://galaxyproject.org/ <http://galaxyproject.org/>`__
.. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg
:target: https://biostar.usegalaxy.org
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
Galaxy Quickstart
=================
Galaxy requires Python 2.6 or 2.7. To check your python version, run:
.. code:: console
$ python -V
Python 2.7.3
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at:
http://localhost:8080
You may wish to make changes from the default configuration. This can be
done in the ``config/galaxy.ini`` file. Tools can be either installed
from the Tool Shed or added manually. For details please see the Galaxy
wiki:
https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
Not all dependencies are included for the tools provided in the sample
``tool_conf.xml``. A full list of external dependencies is available at:
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
Issues
======
Issues can be submitted to trello via the `galaxyproject
website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy
Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__
Galaxy Development
==================
Galaxy welcomes new development! There is extensive documentation on developing
with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__.
Source Repository
-----------------
Galaxy development has moved to `Github
<https://github.com/galaxyproject/galaxy>`__.
**Developers** should develop against the ``dev`` branch in the Github
repository.
**Deployers** can continue to pull Galaxy changes from Bitbucket without
interruption. Alternatively, deployers can track the ``master`` branch in
Github.
Syncing a Fork
--------------
If you fork Galaxy to work on it, you may be interested in keeping your copy
up to date with respect to the main repository. Github has `good documentation
<https://help.github.com/articles/syncing-a-fork/>`__ on this.
.. code:: console
$ git remote add upstream https://github.com/galaxyproject/galaxy
$ git fetch upstream
$ git checkout dev
$ git merge upstream/dev