Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
- Added an option to remove dataset from disk when purging, or leave them for renaming and later removal
- Moved History.purge() and Dataset.purge() methods to the cleanup_datasets.py script
- Eliminated duplicate functionality from admin controller, moving appropriate components to Galaxy reports.
- Re-implemented the long-term process we will use for deleting / purging histories and datasets
(we will initially write external shell scripts to rename dataset files rather then deleting them)
distribution point and copy them to Galaxy's eggs/ directory.
fetch_eggs_tarball.py and check_python_platform.py are mostly for offline
systems. fetch_eggs_tarball.py fetches eggs for your platform (or a
specified platform) and then tars them up, for copying to another system.
check_python_platform.py returns the string for your platform/interpreter
that will be used to download from the egg distribution site.
For those that may have installed revision 2256, use the following SQL command to evolve your schema:
alter table dataset drop column removed;
We have changed direction again on the process we will use to cleanup datasets and histories.
- When we are comfortable with the purge process, the Dataset.purge() function will be modified to delete the file from disk rather than simply renaming it, and the Dataset.remove_from_disk() function will be eliminated.
- The entire process below must be executed at least 1 time ( prior to making these changes ) to ensure that purged files are properly removed from disk. This process is:
delete_userless_histories() -> purge_histories() -> purge_datasets() -> remove_datasets()
Shell scripts have been added for each of these stages with the exception of remove_datasets(), which will eventually be eliminated.
SQL commands to alter schema:
alter table dataset add column removed boolean default 'f';
alter history add column purged boolean default 'f';
- The lifecycle of a history after creation is now deleted -> purged
- Deleting a history will delete all associated datasets (only the database is update, nothing removed from disk).
- Purging a history will purge all associated datasets (datasets are renamed, nothing removed from disk).
- The lifecycle of a dataset after creation is now deleted -> purged -> removed
- Deleting a dataset will only update the database.
- Purging a dataset will rename the file on disk and update the database.
- Removing a dataset will remove the renamed, purged file from disk and update the database.
- Also reverted the behavior of history_delete() to pre-rev 2250 so that no datasets are deleted at teh time the history was deleted by the user.
- The admin controller and the cleanup_datasets.py script include all of the above functionality.
connections
2) Added a script for packing the javascripts, everything is now repacked
with yui-compressor (the packed versions are slightly large, but they
gzip better resulting in an overall reduction).
Nate Coraor