Hello,
I'm not sure this will fix the issue but you might have to use
-p $param_file.params
instead of
-p $params
in your command line.
Best,
L-A
Le 06/02/2012 22:15, Jeffrey Long a écrit :
Hi all,
I am having trouble with what looked to me at first to be a simple
syntactical issue with
Hi Amanda,
I would certainly be interested in using your helpful QIIME wrappers if
you put them on the Toolshed.
Best,
Florent
On 06/02/12 06:22, Amanda Zuzolo wrote:
Hello, all.
I have been working on getting the Qiime scripts into Galaxy as
mentioned before, and they are working with Qiime
Dear colleagues,
I have been struggling with this issue for quite a while now, and I
don't seem to find a solution (neither in situ nor in webo).
here it is:
Because of the confidentiality of our data, I have setup both a Galaxy
server and a UCSC Genome Browser locally on my server. Both
Hello,
I managed to add a new tool coded in bash but I am having some
difficulty adding a tool coded in python.
Here are the contents of the test files:
* Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml :
tool id=test name=Test name
descriptionTest description/description
Sarah:
I've had trouble before with invalid xml files (in your case test.xml)
I don't see an obvious problem with your file, but I've never tried such a
minimal file.
Have a look at galaxy's log during startup to see if it tells you what it
does not like about the file.
Brad
--
Brad Langhorst
Hello Dannon
Could it be possible to have the input dataset's display name appended
to the new history's name instead of plain numbers when the Send
results in a new history option is checked?
This new feature is indeed very useful (thanks a million for it) but
the numbered suffixes
Thanks for the suggestion, I like that! I'll make the change shortly.
-Dannon
On Feb 7, 2012, at 8:03 AM, Louise-Amélie Schmitt wrote:
Hello Dannon
Could it be possible to have the input dataset's display name appended to the
new history's name instead of plain numbers when the Send
Hi Charlie,
Just a minor correction, the Main server is Solaris 10, the clusters on which
jobs run are Debian testing/unstable and RHEL 5.7.
--nate
On Feb 6, 2012, at 9:01 PM, Dannon Baker wrote:
Hi Charlie,
Our main galaxy server is actually running CentOS 5.10. The galaxy cloud
On Feb 6, 2012, at 1:27 PM, Zachary Charlop-Powers wrote:
Hi Galaxy Team,
I am running a small local instance of Galaxy and I've run into a database
error following an upgrade to the Jan27th galaxy-dist release.
The last line when I run run.sh tells me to upgrade my database:
Hello Amanda,
I was just about to embark on EXACTLY this process, so I would certainly be
very interested in saving myself some work.
Would there be any issue (that you're aware of, of course) with using QIIME
1.4.0 instead of 1.3?
-Jeff
On Tue, Feb 7, 2012 at 2:32 AM, Florent Angly
On Feb 7, 2012, at 6:28 AM, Rehan Saleem wrote:
Hi nate ,
thanks for reply , actually i want to know how can i add my own tool in
galaxy , how can i show the output of my postgreSQL function in galaxy just
asume my postgresql database is connected to galaxy . i need the python and
xml
Hi Thon,
The fix for this issue in now available in the central repo in change set
revision 271ccd09bc23. Even though you have a working version of Galaxy, you
should update your instance to at least this revision, and then do the
following as soon as possible.
%sh manage_db.sh downgrade 90
On Mon, Feb 6, 2012 at 6:17 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 6, 2012, at 1:05 PM, Nate Coraor wrote:
On Feb 3, 2012, at 7:30 AM, Peter Cock wrote:
On Fri, Feb 3, 2012 at 11:55 AM, Ryan Golhar
ngsbioinformat...@gmail.com wrote:
'qstat -f | grep jobname' will give you the full
Hello Ira,
Very sorry for the back-and-forth on this. The behavior you encountered was
accurate - the environment in which I was testing was not pristine. I have
committed a fix for this issue in revision b4ba8b20d78d, which is now available
from our central repo.
I started looking at
Hi
I am running into a problem with the scripts/set_metadata.py file since
the last update of galaxy-dist. In this script the name of the universe
file is hard-coded as 'universe_wsgi.ini', see line 44:
config_file_name = 'universe_wsgi.ini' # Safe assumption?
I renamed the universe file in
Thanks for fixing it so fast!
Regards,
Thon
Thon de Boer, Ph.D
Bioinformatics Guru
T: +1.650.799.6839 | E-mail: thondeb...@me.com
http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b
IMPORTANT NOTICE: This email message is legally privileged, confidential and
is for the use of the individual
Rob,
I am not aware that there would be any issue, as I've verified all the
options with the Qiime documentation that is up now (and I've
eliminated those being deprecated).
Amanda Zuzolo
On 2/7/12, Jeffrey Long jlo...@ualberta.ca wrote:
Hello Amanda,
I was just about to embark on EXACTLY
I can't make the call at that time (am in Dhaka) but am very enthusiastic about that effort; please keep me in the loop. I am cc:ing a couple of the people in my lab who also indicated interest in the qiime/galaxy integration effort (though Antonio won't be able to make it either, for the same
I'll be there
Daniel
On Feb 7, 2012, at 10:30, Greg Caporaso gregcapor...@gmail.com wrote:
OK, let's plan on a Skype call at 1pm MT/3pm ET this Thursday (9 Feb
2012). I will initiate the call - my Skype ID is gregcaporaso. Please
let me know if you'd like to join the call, and send my your
Skype ID : patrickgillevet
On Feb 7, 2012, at 12:33 PM, Daniel McDonald wrote:
I'll be there
Daniel
On Feb 7, 2012, at 10:30, Greg Caporaso gregcapor...@gmail.com wrote:
OK, let's plan on a Skype call at 1pm MT/3pm ET this Thursday (9 Feb
2012). I will initiate the call - my Skype
That's great news! Thanks for checking.
Rob
On Feb 7, 2012, at 10:59 AM, Amanda Zuzolo wrote:
Rob,
I am not aware that there would be any issue, as I've verified all the
options with the Qiime documentation that is up now (and I've
eliminated those being deprecated).
Amanda Zuzolo
OK, let's plan on a Skype call at 1pm MT/3pm ET this Thursday (9 Feb
2012). I will initiate the call - my Skype ID is gregcaporaso. Please
let me know if you'd like to join the call, and send my your skype id.
Looking forward to talking about this!
Greg
2012/2/7 Rob Knight
I've upgraded my developmental Galaxy instance to the latest galaxy-dist
release with a transplanted the drmaa.py patch from galaxy-central. All .conf
files have been updated. However, I can't start the instance now The error
listed below is generated. I tried enabling/disabling the toolshed
Hi Alex,
If your migration scripts through 90 executed cleanly, then your
tool_shed_repository.uninstalled column should exist as that column is created
in the 0090 script. What was the log of your db migration upgrades that
occurred when your database was migrated from version 85 to 90?
$ sh manage_db.sh -c ./dev_universe_wsgi.runner.ini upgrade
85 - 86...
Migration script to add the metadata, update_available and includes_datatypes
columns to the tool_shed_repository table.
done
86 - 87...
Migration script to create the tool_id_guid_map table.
done
87 - 88...
Migration script
Dear all,
I have a working module which generates wig files for genomic annotation
from a single column of a bigger input data matrix (Input A). In the
current state, the user has to input the column name (Input B) from
which to calculate the values in the wig file.
Now I'd like to modify the
Alex, this is strange, so it'll be tricky to figure out what's causing the
problem. I can't think of anything that would cause this unless 2 different
databases are somehow being used. I assume your database configured in your
file dev_universe_wsgi.runner.ini is the same as the database
Greg,
Startup log:
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 16:13:29,613 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-07 16:13:29,614 Loaded
reference to tool shed: Galaxy main tool shed
Hi Greg,
Thanks for that fix ... I'll check it out.
I think the issue of sniff order is a pretty important one for shed tools that
require proprietary datatypes. The problem is that galaxy's default sniffers
include some extremely generic sniffers (eg text,xml) which will catch pretty
much
Ira,
Thanks for the feedback - I'll come up with something that allows for
proprietary sniffers to be loaded first and let you know when it's available.
It shouldn't take me too long. I will probably continue to keep the rule of
ignoring conflicts in proprietary datatypes, so sniffers for
Hi Greg,
Thanks .. that sounds like a good solution. I'll be happy to test it when its
ready.
Ira
On 08/02/2012, at 10:22 AM, Greg Von Kuster wrote:
Ira,
Thanks for the feedback - I'll come up with something that allows for
proprietary sniffers to be loaded first and let you know when
Dear Greg,
In the latest version of the galaxy-central code there seems to be a bug
preventing me from updating my tools. When I go to update a tool I get the
following error
URL:
Thanks Ira, I'll have this fixed tomorrow and let you know. Sorry for these
glitches, we'll get these things ironed out rapidly. Thanks for helping!
On Feb 7, 2012, at 7:40 PM, Ira Cooke wrote:
Dear Greg,
In the latest version of the galaxy-central code there seems to be a bug
Dear Sir or Madam,
I am installing a galaxy server on CentOS with UCSC Genome Browser mirror site.
The mirror site works well. I installed the galaxy in the same server.
Now my question is: how to set up httpd.conf file so I can access both
websites(UCSC Genome Browser, and Galaxy) remotely?
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