[galaxy-dev] GALAXY LOCAL INSTALLATION: Remove history

2013-07-01 Thread Rafael Hernández
Hi Galaxy devs,

I've installed Galaxy in local and I see that in spite of the users remove
their histories using the Delete history option, the used space is not
free.

As I understand reading the Galaxy documentation, after deleting the
history, the history is marked as Deleted but files are not removed.
After 60 days, Galaxy automatically remove them.


1. If you delete a specific history using the **Options** link at the
top of the history panel, that history and all of its associated datasets
will be removed from disk 60 days after you deleted the history.
2. Those specific history items ( datasets ) that you delete from one
of your histories by clicking the X icon in the history item will be
removed from disk after 60 days, but unless you manually delete your
history, you will still be able to view the history itself ( only the
dataset that you deleted from your history will be removed from disk ).


I suppose this should be the default behavior too for local installations.
but I did not configure anything about that and I need to confirm this is
true because the used space becomes bigger each day!

Is there any way to change this periodicity to less days?

Thank you and regards,

Rafa Hernández de Diego

Genomics of Gene Expression Lab.
Bioinformatics and Genomics Department
Prince Felipe Research Centre (CIPF)
C/ Eduardo Primo Yúfera 3
46012 Valencia, Spain
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] GALAXY LOCAL INSTALLATION: Tools and Data

2013-02-20 Thread Rafael Hernández
Hi,

I've installed Galaxy in local and following the Tool
dependencieshttp://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
manual
I installed all necessary tools. However for some of then such as BWA,
Bowtie,... it's usually needed to create indexes.

Where should I store those indexes? In the galaxy directory or in each tool
directory? How can I tell galaxy where the indexes are?
I find a manual's page talking about it /
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup), suggesting
to organize the various index files for each build, but I don't know if
these folders should be stored into Galaxy directory (eg. in tool-data
directory) or what.

Could you please explain this a little?

Thank you and regards,

Rafa Hernández de Diego

Genomics of Gene Expression Lab.
Bioinformatics and Genomics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/ Eduardo Primo Yúfera 3
46012 Valencia, Spain
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/