mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-31 02:28:09 +08:00
mvdbeek
abe404539e
``Repeat.get_initial_value`` passed the parent ``context`` directly to
each child input's ``get_initial_value``, so siblings within a repeat
instance were invisible to each other's ``dynamic_options`` lookups.
``Section`` and ``Conditional`` already wrap their partial ``rval`` in
a child ``ExpressionContext`` for this reason — bring ``Repeat`` in
line.
Surfaced by ``data_manager_manual`` (``min=1`` on both the outer
``data_tables`` repeat and the inner ``columns`` repeat). The inner
``data_table_column_name`` select declares::
dynamic_options="galaxy_code_get_available_data_table_columns(
__trans__, data_table_name)"
During the initial ``populate_state`` pass ``Repeat.get_initial_value``
built the default ``data_tables`` instance with the outer
``rval_dict`` only visible as a local variable; the recursive
``columns.get_initial_value`` call therefore saw a context that did
not contain ``data_table_name`` and the eval raised::
NameError: name 'data_table_name' is not defined
The error is caught at ``basic.py`` (logged at DEBUG, options returned
as ``[]``) and the default instance is later discarded by
``_populate_state_legacy`` which rebuilds the state with a proper
child context — so the tool ran fine, but every form build polluted
the log.
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.10 or higher. To check your Python version, run:
.. code:: console
$ python -V
Python 3.10.12
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
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .