mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-29 17:42:12 +08:00
mvdbeek
1a43ef5b83
I'm not sure how/why this happens, but this can be reproduced by copying a file to a location in one process, while checking the size in another process:
Run this to copy a file indefinitely:
```
import os
import shutil
open('test').write("foo")
while True:
shutil.copy('test', 'test.file')
os.remove('test.file')
```
In the same directory run this
```
import os
count = 0
wrong_size = False
while True:
try:
size = os.path.getsize('test.file')
if size == 0:
wrong_size = True
wrong_count = count
elif wrong_size and os.path.getsize('test.file') != 0:
# We have seen the wrong size being reported, but now it's correct again
print("Got wrong file size at %dnd try, was fixed in %dnd try" % (wrong_count, count))
break
except Exception:
pass
count += 1
```
It'll (probably) fail like this:
```
Got wrong file size at 0nd try, was fixed in 1nd try
```
or more often:
```
Got wrong file size at 31nd try, was fixed in 32nd try
```
This seems to be fixed when running os.path.getsize() another time,
so we simply do that here.
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__
.. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg
:target: https://biostar.usegalaxy.org
:alt: Ask a question
.. 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/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. 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 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
Configuration & Tools
=====================
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 `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>`_ .
Roadmap
=============================
Interested in the next steps for Galaxy? Take a look at the `roadmap <https://github.com/galaxyproject/galaxy/issues/1928>`__.