Hi,
I am sorry for the trivial question. Does anyone know how I can make a local
instance of Galaxy use our local database files? We have downloaded the
database from USCS and would like to use the downloaded files instead of
retrieving it from the UCSC Table Browser when processing data.
1) The dist is most recent:
[galaxy@galaxy galaxy-dist]$ hg tip
changeset: 7982:12fcd068b12e
tag: tip
user:Daniel Blankenberg d...@bx.psu.edu
date:Thu Oct 18 11:22:12 2012 -0400
summary: Do not hide failed datasets with HideDatasetAction post job
action.
2)
Hi Alex
As posted earlier there were problems with our instance of which some are
sorted but one did not. The change attribute failure...
Since the instance was empty anyway we decided to do a fresh pull and start all
clean (also a clean MySQL db).
It all works ok on SQLlight and when
Hi Mathieu,
As I mentioned in my previous email, here is the select that is needed. I need
to see the values of all columns for the mothur_toolsuite row.
select * from tool_shed_repository where name = 'mothur_toolsuite';
On Nov 13, 2012, at 7:33 AM, Mathieu Bahin wrote:
Hi Greg !
Hans-Rudollf
Thanks and I know it is a bunch of output...sorry about that I will perform
the two queries.
Regarding the MySQL or postgresI am used to the mysql dialect.is that
wrong :-)
But if it is for the galaxy server only we might want to go to postgreSQL
good idea if
Sent from my Verizon Wireless BlackBerry
-Original Message-
From: Rolando Mantilla rolandomantil...@gmail.com
Date: Mon, 12 Nov 2012 19:31:20
To: galaxy-u...@lists.bx.psu.edu
Subject: Warning message
I'm having issues with the FASTQ_Groomer. What I have done it first
I downloaded an
It looks like you have conflicting blastxml entries. Edit your
datatypes_conf.xml to remove any references to blastxml (the toolshed manages
datatypes separately), restart galaxy, and you should be good to go.
-Dannon
On Nov 13, 2012, at 9:19 AM, rolandomantil...@gmail.com wrote:
Sent from
On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote:
On Nov 12, 2012, at 2:35 PM, Bossers, Alex wrote:
Nate,
crapthat fixed it...not sure why that setting didn't show up in the svn
diff but anyway...it's working again.
I wonder; if a user is member of two groups with different
Hhhmmm just tested this and indeed a compressed 10GB export history file of the
previous instance (expanded roughly 30GB) does not seem to contribute to the
history size used for a user when imported again The files are physically
there and checking physically on disk it indeed consumes
Nate
Thanks. The latter we noticed. Indeed the largest associated seems to be
used
We are currently investigating another probable issue with the quota. When you
import an history it doesn't seem to count to the space used. But we are
testing this more thoroughly
Alex
So from what I am reading it is either not creating or prematurely
deleting this working directory? I will mod that option and see if I can
prevent it from deleting.
AC
On 11/12/2012 2:11 PM, Nate Coraor wrote:
On Nov 12, 2012, at 11:17 AM, Alan V. Cowles wrote:
yeah I'm not seeing the
I tried to reply to similar posts, but couldn't figure out how to do it.
So posting again:
Galaxy giving this error when editing workflow, just after creating
workflow from existing history:
URL:http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148
Hi Greg !
Running the sql command, I got that (actually, it's 'mothur_toolsuite' so I
change a bit the request but it is not deleted):
mysql select name from tool_shed_repository;
++
| name |
++
| mothur_toolsuite |
| protk |
| roche454_toolsuite
Hi again,
Sorry for the mistake in the request, but I think that now we spotted the
problem more precisely.
When I install 'mothur_toolsuite', the 'metadata' field is set with a long JSON
value (length 68,000). We noticed that when suppressing the tool, this value
is truncated around a
Thanks Jeremy and Brad. I have made some good progress. The code below works
but does not give a newname.
It needs this to work:
'runtool_btn': 'Execute',
is a required parameter in the various checks (there is also validation code
there for a URL origin parameter too).
The code below works
Richard,
This is fixed as of 5013377e0bf7. This may not be in the next distribution,
but will be in the one after that. Of course, you can manually pull the change
at any time.
-Dannon
On Nov 9, 2012, at 4:20 PM, Richard Park rp...@bu.edu wrote:
Hi Guys,
I updated to the latest galaxy
Sanjar,
This is fixed as of 5013377e0bf7. This may not be in the next distribution,
but will be in the one after that. Of course, you can manually pull the change
from galaxy-central at any time.
-Dannon
On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote:
I
Hello all,
Just a reminder that the November GalaxyAdmins web meetup is tomorrow,
Wednesday, at 10 am central US time. Details are below.
Please join us,
Dave C
On Mon, Nov 5, 2012 at 3:28 PM, IIHG Galaxy Administrator
iihg-galaxy-ad...@uiowa.edu wrote:
Hello,
The next meeting of the
One dataset I want to view in Trackster has an error
ConverterDependencyException: 'A dependency (bgzip) was in an error state.
I've seen this once or twice before but haven't been able to track down the
issue yet.
Here are two workaround that may help you out:
(1) Add the dataset to a
Two ideas:
(1) Use data libraries to import all UCSC data files, making sure to link data
rather than copy into Galaxy:
http://wiki.galaxyproject.org/Admin/Data%20Libraries/Uploading%20Library%20Files
(2) Set up a local table browser and modify the ucsc_tablebrowser.xml to point
to your local
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