Hi Tomas,
I am going to move your question over to the galaxy-...@bx.psu.edu
mailing list, which give it better exposure to the development
community. This is where you will also want to post questions about
local installs going forward. Someone here may have advice about this
tool - but real
Correct; certain NSG tools require additional configuration for their
indices (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)
On Tue, Mar 5, 2013 at 1:07 PM, shenwiyn wrote:
> **
> Hi,
> I've installed Galaxy in local as what Rafael does.I want to make sure
> that the basic functions
The tools API, incomplete as it is, could be used to automatically generate a
list of tools for a single instance.
J.
On Mar 4, 2013, at 5:37 AM, Hans-Rudolf Hotz wrote:
>
>
> On 03/03/2013 05:18 PM, Dave Clements wrote:
>> Hi Bernardo,
>>
>> I'm intrigued by this idea. It might be possible
Hi,
I've installed Galaxy in local as what Rafael does.I want to make sure that the
basic functions work successfully just depending on the necessary tools in Tool
dependencies manual,and the NGS tools not only depend on the necessary tools
but also some another needed data(such as indexes,and s
Hi Dannon,
I understand that instead of having one dataset with multiple files you are
planning to use existing datasets and combine them in a 'collection'. My
concerns are:
1. Our data consists of 200-8000 files, can you imagine how many datasets we'll
end up with? It will be a mess.
2. All t
I've already terminated the cluster, since it was for short term use.
It is strange that the admins were not on the user list.
Would you provide some hints for next time re-launching instance, if the same
thing happens?
Kathryn
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Sunday, Marc
Nevermind, I noticed that the wiki page on Install galaxy was recently
updated to show how to do this.
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan
Sent: Monday, March 04, 2013 9:50 AM
To: 'Nate Coraor';
Hi Nate,
I have checked and I am indeed in the Default branch. Is there an easy way
to switch over to the stable branch via command line?
-Kelvin
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: Monda
Dear all,
Our galaxy suffers from frequent hickups, which apparently are due to broken
pipes.
It will give these errors in paster.log
Exception happened during processing of request from ('127.0.0.1', 53234)
Traceback (most recent call last):
File
"/us
Hi all,
it seems my clean-up enthusiasm caused some inconsistencies with datasets'
deleted status. I encounter the following phenomenon: datasets appear totally
fine in the data libraries, but once they are loaded into a history, they
appear as deleted there.
I dug through the database and fou
All,
Could you check whether you are running the "default" or "stable" branch of
galaxy-dist? You can find out with the `hg branch` command. I believe this
problem should only exist if you're running the "default" (development) branch,
which is not recommended.
Thanks,
--nate
On Mar 4, 2013
Hi,
I completely agree with Hans proposal. Creating a new page to list all the
tools would be a good alternative. In addition, this page could offer
categories of bioinformatic tools and more information of the tool in
question. Nevertheless, a Google search box is a very good starting point.
The
Shenwiyn,
I have not been able to duplicate that error message in my local
environment, what changeset revision of Galaxy are you running, and how
is your server environment configured?
--Dave B.
On 3/4/13 10:41:36.000, shenwiyn wrote:
Hi,
I want to install our local Galaxy for more than
Hi,
I want to install our local Galaxy for more than one users. When I want to
install some tools from tool shed via admin user ,and I followed the
instructions in the follow link:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_lo
On Mon, Mar 4, 2013 at 3:16 PM, John Chilton wrote:
> Hi Alex and Peter,
>
> I appreciate the comments, but I am not going to keep talking about
> this issue here, I consider the issue closed. The Galaxy team has
> spoken clearly on this topic. They have accepted dozens of my pull
> requests and
Hi Alex and Peter,
I appreciate the comments, but I am not going to keep talking about
this issue here, I consider the issue closed. The Galaxy team has
spoken clearly on this topic. They have accepted dozens of my pull
requests and I am very happy about all of them, and I need them to
accept do
Unfortunately the snapshotting process used by the is really slow, as
you've noticed, and there's not much we can do to make that faster. We've
discussed other methods for growing the filesystem but haven't finished it
yet.
For working with S3, instead of s3fs you're more than welcome to give
Gal
On Mon, Mar 4, 2013 at 7:59 AM, Hans-Rudolf Hotz wrote:
> @ Dannon
>
>
> > While we definitely do recommend that if you have the option to
> > choose, go with postgres, Galaxy should function both now and in the
> > future with MySQL. In this case, your galaxy will function just fine
> > without
Hi Hans,
Thanks for "bumping" this thread. The issue has been fixed in development and
will be included in the next release.
--nate
On Mar 4, 2013, at 5:48 AM, Hans-Rudolf Hotz wrote:
> Hi Lance
>
> I was just running into the same issue as part of upgrading our production
> server from rel
Alex,
To reiterate what Jeremy has already said on the mailing list, this is
definitely something we want, and need, for Galaxy. While this particular
implementation has a lot of good parts, creating these collections as
first-class composite datasets isn't ideal and we'd be stuck supporting
them
Hi Derrick and Dannon
@ Derrick
Yours happened when upgrading from 108 - 109 (which didn't happen to me).
If you have a chance to upgrade to release_2013.02.08, your database
will be upgrade from 109 - 110, I am very interested to see if the index
creation error happens to you as well.
We
On Fri, Mar 1, 2013 at 2:55 PM, Peter Cock wrote:
> Hello all,
>
> Re: BitBucket Issue 538 - Admin action to reload ".loc" files without
> restarting Galaxy
> https://trello.com/card/538-admin-action-to-reload-loc-files-without-restarting-galaxy/506338ce32ae458f6d15e4b3/475
>
> Currently Galaxy ad
Hi all,
I've retitled this from "Composite datatype output for Cuffdiff" to
"Implementing dataset collections" to try and link into Jeremy's thread.
References:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013634.htm
Hi Lance
I was just running into the same issue as part of upgrading our
production server from release 2012_10_05 to 2013_02_08 (unfortunately,
I didn't catch it last week, when I did our test server, as the job
limit was not set there).
I added a little comment to your trello "ticket", bu
On 03/03/2013 05:18 PM, Dave Clements wrote:
Hi Bernardo,
I'm intrigued by this idea. It might be possible to build a Google
custom search, similar to the Tools tab of the usegalaxy search
(http://galaxyproject.org/search/usegalaxy/). That's would not be an
ideal solution, but it would be qu
25 matches
Mail list logo
