On Thu, Jun 9, 2011 at 4:20 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter Cock wrote:
Hi Nate,
Since you're looking at this kind of thing, would the Saved Histories
page be worth updating to show the size on disk of each history? As
a Galaxy user that seems moderately useful - although
On Thu, Jun 16, 2011 at 3:00 AM, Ravi Madduri madd...@mcs.anl.gov wrote:
I apologize for jumping on to this thread a bit late. I read below that
there is a plan to pull tools into a galaxy installation automagically. I
wonder if you plan on providing some kind of API to query the tool registry
Hi all,
I just tried updating one of my tools on the new hg based Galaxy Tool
Shed and ran into some issues. I guess I'm the first person to try
this...
First of all, there is no clear update action like there used to me.
Could that be restored please?
I'm building a tool that needs the display name of a file inside the
output of the tool.
To clarify, I have a tool that merges gene expression result from cufflinks
for many samples. It generates a matrix tab-delimited file that provides
the results with genes or transcript down one axis and
Hi Peter,
If you were curious it was fixed about 7 hours later in 5681:0886ed0a8c9f
Thanks for using Galaxy,
Dan
On Jun 16, 2011, at 4:32 AM, Peter Cock wrote:
On Wed, Jun 15, 2011 at 4:56 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dan,
I just started work on updating my MIRA
On Thu, Jun 16, 2011 at 2:23 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
If you were curious it was fixed about 7 hours later in 5681:0886ed0a8c9f
Thanks for using Galaxy,
Dan
Thanks - I know this kind of unexpected breakage is inevitable sometimes,
but would recommend tool
Hi Peter,
Production servers, or any server where you have users, should always track
Galaxy-dist.
Galaxy-central is a development repo (you get access to the latest and
greatest, but also should Expect more bugs to pop up at any given time), from
the Galaxy-central header on bitbucket: Main
On Thu, Jun 16, 2011 at 3:01 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Peter,
Production servers, or any server where you have users, should always track
Galaxy-dist.
Yes, that's very clear.
Galaxy-central is a development repo (you get access to the latest and
greatest, but also
Any other ideas? I can run galaxy-central but I'd like to work with the stable
galaxy if possible.
Because earlier revs of galaxy-dist startup fine for me I went through the
exercise of using hg bisect to mark my last pull rev of 5355 as good and 5585
as bad I went through some revs, each
Hi Peter,
On Jun 16, 2011, at 10:10 AM, Peter Cock wrote:
On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Peter,
I've added comments to each of these issues in bitbucket, and have pated
them inline below as well.
On Jun 16, 2011, at 5:03 AM, Peter Cock wrote:
Hi
Michael Steder wrote:
Any other ideas? I can run galaxy-central but I'd like to work with the
stable galaxy if possible.
I can rebuild the bx_python egg, but it's odd this is happening - the
old numpy eggs haven't changed in over a year. Could you remove
~/.python-eggs, and the bx_python and
Yes. But right now it is kind of a hack to do sudo in the condor runner. We are
working on integrating this with Globus online's (www.globusonline.org)
identity and group management capability to make it more flexible.
On Jun 15, 2011, at 8:40 PM, Chorny, Ilya wrote:
Ravi,
Do your galaxy
I tried the following:
$ rm -rf ~/.python-eggs/
$ cd galaxy-dist
$ rm -f ~/eggs/*
$ sh run.sh
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg
Fetched
Hello Joe,
I've enhanced the feature for defining sample form rows in change set
5716:6e1576c83456 (currently available only in our development repo, but will
be available in the distribution shortly) to include the ability to include
field values (in addition to field names) when defining
Michael Steder wrote:
I tried the following:
$ rm -rf ~/.python-eggs/
$ cd galaxy-dist
$ rm -f ~/eggs/*
$ sh run.sh
Some eggs are out of date, attempting to fetch...
Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg
Fetched
On Jun 16, 2011, at 9:55 AM, Nate Coraor wrote:
Arright, I'm running out of ideas, the same platform and python version
on a fresh checkout works fine for me and the other developers.
Could you remove just your bx_python egg and then scramble it locally:
% rm -rf eggs/bx_python*
%
On Thu, Jun 16, 2011 at 3:26 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
I understand, and that is why I am working feverishly to add features
that do not force the use of hg form the command line (I've got several
features functional, but not everything yet). The current tool shed
Does anyone have practical information for installation and set up for the
galaxy distribution on a cluster??
Robert C. Jackson
Software Systems Specialist III
The University of Texas Pan-American
Computer Support Services
Division of Information Technology
Phone: 956-665-2455
Fax: 956-665-8777
On Thu, Jun 16, 2011 at 4:31 PM, Robert Jackson rj...@utpa.edu wrote:
Does anyone have practical information for installation and set up for the
galaxy distribution on a cluster??
Did you not get these replies?
http://lists.bx.psu.edu/pipermail/galaxy-user/2011-June/002715.html
On Jun 16, 2011, at 10:23 AM, Peter Cock wrote:
On Thu, Jun 16, 2011 at 3:26 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Jun 16, 2011, at 10:10 AM, Peter Cock wrote:
Are you expecting tool authors to work primarily at the hg level?
You didn't answer that one ;)
Not
On Thu, Jun 16, 2011 at 5:40 PM, Chris Fields cjfie...@illinois.edu wrote:
I'm of the opposite mind; I'm not sure there is an absolute need to
have one's tools be a branch or fork of the main tool shed, though
I agree there is also utility in allowing that (having a customized
'main' repo, or
Matt,
I'm moving your Trackster question onto the galaxy-dev list:
one issue I keep running into is that it's not super clear how to go about
configuring the dynamic tracks you showed off in your talk.
Is there some guidance somewhere that I am missing on this? I confess my own
motive
Henry,
I'm moving this over to galaxy-dev since it has to do with a local
instance.
It definitely sounds like you've got things set up right. You don't
say what the result of your run is--is it successful (green) but an
empty file? Or is there an error? If it's empty, it's possible your
Hi Kelly and others,
Thanks for the move. The SRMA run doesn't seem to go to completion; instead, it
stays yellow and produces no output (the corresponding dataset is 0KB).
I did try the second test in srma_wrapper, and here is the error I got:
Traceback (most recent call last):
File
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