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 "/Users/u
I figured it out!
The mistake I was making was assuming that I needed to use the "metadata"
attribute. I found in the "Data" base class that there is a display_name
method.
So instead in my xml I just used the syntax $input.display_name and I got
exactly what I was looking for.
Are things like
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
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
> moti
On Thu, Jun 16, 2011 at 5:40 PM, Chris Fields 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 optimizing tools
On Jun 16, 2011, at 10:23 AM, Peter Cock wrote:
> On Thu, Jun 16, 2011 at 3:26 PM, Greg Von Kuster 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 ;
On Thu, Jun 16, 2011 at 4:31 PM, Robert Jackson 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
http://lists.bx.psu.edu/pi
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 3:26 PM, Greg Von Kuster 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 necessarily, but hg is the basis for uploading and do
On Thu, Jun 16, 2011 at 3:26 PM, Greg Von Kuster 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 requires
>
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*
>
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
> http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2
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 samp
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
http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-macosx-10.6-uni
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
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 an
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 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 a
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 time
On Thu, Jun 16, 2011 at 3:01 PM, Daniel Blankenberg 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 should Expec
On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster 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 all,
>>
>> I just tried updating one of my tools on the new hg based G
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: "Mai
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 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
On Thu, Jun 16, 2011 at 2:23 PM, Daniel Blankenberg 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 developers i
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 wrote:
>> Hi Dan,
>>
>> I just started work on updating my MIRA wrapper, and fell over
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
Hello Martin,
Nice to see you over here :) I just managed to fix my own issues with
the "module system" this morning, maybe it'll be useful for you:
unset PYTHONHOME
But that would probably require more work on your side (a.k.a, setting
virtualenv):
$ module list
No Modulefiles Currently Loaded
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?
https://bitbucket.org/galaxy/galaxy-centra
On Thu, Jun 16, 2011 at 3:00 AM, Ravi Madduri 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
> and discover th
On Thu, Jun 9, 2011 at 4:20 PM, Nate Coraor 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 perhaps m
On Wed, Jun 15, 2011 at 4:56 PM, Peter Cock wrote:
> Hi Dan,
>
> I just started work on updating my MIRA wrapper, and fell over a
> regression present of 6079:5e6254f2b9e3, steps to reproduce on Linux:-
>
> 1. Install latest Galaxy
> 2. Install my MIRA wrapper v0.0.1 from the tool shed (don't need
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