Hi,
On 26.03.2012 17:14, Nate Coraor wrote:
On Mar 22, 2012, at 12:30 PM, Alfonso Núñez Salgado wrote:
Hi Andreas:
As far as I know Galaxy is designed to manage its own users and not to be
integrated in any other platform. I think that the idea is to use galaxy as
another user of your
Hi Dannon,
Unfortunately our server is (still) behind a firewall, so I can't share
anything, but I hope you can reproduce the error from the following
description.
If I make a vanilla test workflow say:
Input Dataset - Map with BWA for Illumina (single end) - SAM-to-BAM -
flagstat
and
An extension on the problem to get Toolshed to start.
On my 'sandbox' machine, I can launch toolshed now.
But on our test-production, running run_community.sh now still fails,
complaining mercurial is not installed.
But on this system (Centos5), I have problems to install mercurial for
Le 27/03/2012 11:03, Louise-Amélie Schmitt a écrit :
Le 26/03/2012 16:13, Nate Coraor a écrit :
On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote:
Hello everyone,
I wanted to start the drmaa job runner and followed the instructions
in the wiki, but I have this error message when I
Greg,
1. The horizontal rule dividers specified by a - in the text have
disappeared.
Fixed in galaxy-central changeset cb5ff5b1bd67
2. Also I spotted a change where this ..
- line 1 of some bullets
- line 2 of some bullets
Following line.
.. lost the blank line after the line
Hi everyone,
The drmaa runner literally floods the Galaxy output with its own output
(dozens of lines every second) which makes the Galaxy log impossible to
read. Would there be a way to separate the two of them? I tried to look
into the code but I'm not fully sure about what exactly produces
The new look will go out with the next galaxy-dist, once we've squashed most of
the bugs. Thanks for your interest!
On Mar 26, 2012, at 5:18 AM, Leandro Hermida wrote:
Dear all,
How do I get the new Galaxy look enabled that you see in
usegalaxy.org? I have two servers on the latest
Hi,
I would like to know which tool_conf.xml to use, and would like to know the
difference between the main and the sample one. I know that the functional
tests are running against the tool_conf.xml.sample but what tool_conf.xml.main
is used for?
Thanks.
Anne.
--
Anne Pajon, Ph.D.
Cancer
Hi,
I have set up a brand in my universe but with the new look you cannot see it
as it is written on top of the Tools' header. The new look is available from
galaxy-central.
Thanks,
Anne.
On 27 Mar 2012, at 15:24, James Taylor wrote:
The new look will go out with the next galaxy-dist, once
Hi Nate,
Thanks for your answer. I am looking forward at the relocation of the tools to
the tool shed then.
Cheers,
Anne.
On 26 Mar 2012, at 14:49, Nate Coraor wrote:
Hi Anne,
We're aware that many tests require certain local data to be set up
beforehand. As such, these tests can't
On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote:
Hi,
I would like to know which tool_conf.xml to use, and would like to know the
difference between the main and the sample one. I know that the functional
tests are running against the tool_conf.xml.sample but what
tool_conf.xml.main is
Hi Greg,
I did not get any answer unfortunately. I still do have errors when running the
functional tests and I do not know how the tool shed will solve the problem as
Nate replied to a related email regarding functional test failures.
As far as I am aware, the most used tool for comparing the
Hi Nate,
Thanks but I am still confused... sorry. Why these two files are different
then? Are you not running the functional tests on all the tools available at
the public server?
Anne.
On 27 Mar 2012, at 16:33, Nate Coraor wrote:
On Mar 27, 2012, at 11:17 AM, Anne Pajon wrote:
Hi,
I
We have a buildbot set up that runs our functional tests against various
platforms / environments. The .sample file used by the buildbot tests
everything. The tool_conf.xml.main contains a subset of everything that is
tested.
On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote:
Hi Nate,
Got it. Thanks!
On 27 Mar 2012, at 16:53, Greg Von Kuster wrote:
We have a buildbot set up that runs our functional tests against various
platforms / environments. The .sample file used by the buildbot tests
everything. The tool_conf.xml.main contains a subset of everything that is
Hi Lisa,
The implicit conversion of your BED file to a GeneTrack file failed. The usual
cause for this is a missing dependency such as tables or hdf5. Running the
converter in a standalone mode (click on the pencil icon for the bed dataset
and look for 'convert') should give some more
I wrote a script to compare these files mainly to be able to remove tool's
sections and add our own, but when used to compare main vs sample I've got 2
sections and 3 tools that are in main but not in sample. Here is the list:
WARNING: --- cshl_library_information: Section from
Hi,
I have installed the local galaxy and tried to run draw quality score boxplot.
It showed the error message:
Could not find/open font when opening font arial, using internal non-scalable
font
Could you please tell me how to fix it ?
Thanks,
Jianpeng
Hello,
We are going to migrate to a new instance of the galaxy server. Our current
instance contains a number of workflows and other data that we would like
to have available on the new server. Is there a way to backup the workflows
and then reload them on the new server?
Regards,
-Robert Paul
You first need to find where on your Galaxy server the fonts are for gnuplot.
An example is /usr/local/share/fonts/msttcorefonts. Once you know the
directory, you can set an environment variable for your Galaxy user, like this:
export GDFONTPATH=/usr/local/share/fonts/msttcorefonts
Place
You can use $input.name to get the name you see in the history.Unfortunately, that usually is something silly like "Samtools on data 3"I have changed all the labels for all the major file that are produced to provide more sensible names, usually based on the input...An example below is how I
Thanks for addressing this...The workflows load MUCH faster now...ThonOn Mar 20, 2012, at 07:54 AM, Dannon Baker dannonba...@me.com wrote:Hi Thon, Thanks for reporting this. I see what the problem is here at least for the clone duplication, and I've committed a fix in 6833:e8e361707865 that will
Jeremy,
Thanks. The horizontal rule is working for me now.
An example of the second item is attached in XML file. The last list at the
bottom doesn't render a blank line after the last list item, but used to.
Rgds,
Greg
On Tue, Mar 27, 2012 at 11:51 PM, Jeremy Goecks
Kory,
Cufflinks quantifies transcripts in parallel, and the inconsistencies that
you're seeing are likely the result of these processes finishing in different
order during different runs. To address this issue, you can use the Galaxy sort
tool.
Ultimately, this is not a Galaxy issue but an
Enis,
Thanks, your instructions below worked ok and I have reduced my 700GB to 1
GB.
No doubt a pile of genome tools don't work now but I don't need them.
I see this is described in the Wiki as well, but it was more concise below,
thanks.
cp -r was fine for copying the remnants of
Awesome! Also glad to hear your rate of success can be quantified as a 700%
improvement. Amazing! :)
Best,
Enis
On Wed, Mar 28, 2012 at 2:57 PM, Greg Edwards gedwar...@gmail.com wrote:
Enis,
Thanks, your instructions below worked ok and I have reduced my 700GB to 1
GB.
No doubt a pile of
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