Here is the first part of the error (Traceback):
galaxy.tools ERROR 2013-08-01 22:56:16,590 Exception caught while
attempting tool execution:
Traceback (most recent call last):
File
"/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py",
line 1936, in handle
Hello,
My local cluster based galaxy installation was running fine till this
evening. Later I decided to test some workflows and got an error with
massive stack trace.
I can't make any sense of this. Here is the last part of the error. The
stack trace is literally 1000's of lines. Can somebody
Hi Piotr,
Regarding "data parallelism" - Galaxy can split a single large file into small
parts and process them in parallel, then merge outputs into single file.
That's not what we need, as we already have multiple input files. But as I
understand, there's a possibility to write our own splitte
The new volume update hasn't been released yet to fix those tool issues,
but the existing volume should actually appear in /mnt at launch.
On Thu, Aug 1, 2013 at 4:28 PM, Ravpreet Setia wrote:
> Thanks for letting me know, my old credentials have been disabled.
>
> Anyways, that is all the log
Thanks for letting me know, my old credentials have been disabled.
Anyways, that is all the log contained. I clicked on "show all". Does
launching it with this method work on your end?
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu
Here it is:
'pd.yaml' not found at paths.py load!
Set paths.P_GALAXY_HOME as '/mnt/galaxyTools/galaxy-central'
Python version: (2, 6)
Image configuration suports: {'apps': ['cloudman', 'galaxy']}
[DEBUG] app:54 2013-08-01 20:07:40,138: Initializing app
[DEBUG] app:55 2013-08-01 20:07:40,138: R
Peter,
As of 10290:d34d6d1da813, nsltradamus and effectivet3 should start
returning valid test results. As for seq_rename, it looks like the
columns in four_human_proteins.rename.tabular are not being detected
correctly, even though they are tab separated. I'll continue to
investigate, and le
Hi Ricardo,
do you run velvet on your own cluster with SGE? Sometimes, "No Peak
found" can also mean that velvet used to much resources and was killed
by your cluster engine. In that case it often happens to us that we get
no result. A solution is a give velvet more resources or adjust the
resourc
Dear all,
Today when running velvet oprimizer vlsci, we encountered that if you use two
long files as input then the output is a file that its description is "no
peek". However when I run the files seperately the velvet optimizer seems to
work fine. I am not sure if this is a bug or not.
Tha
Also check
http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn which
includes indices for Bowtie2 [see ftp://ussd-ftp.illumina.com/README.txt].
From: shenwiyn mailto:shenw...@gmail.com>>
Reply-To: shenwiyn mailto:shenw...@gmail.com>>
Date: Thursday, August 1, 2013 3:17 AM
To:
It shouldn't, unless the root cause of that error also affected the FTP
transfer. Does FileZilla say there are any transmission errors?
On Thu, Aug 1, 2013 at 1:16 AM, Mark Edward Fabreag wrote:
> Good day!
>
> While I was uploading the file (through FileZilla), I encountered this
> message box
Hi Jorrit,
Thank you for your explanation. Would you be able to give us an example of what
do you mean by fractions and when the task_%d are being used to pick files.
Just want to make sure we have good understanding of the problem that you
solved.
Also, I vaguely remember seeing 'data parallel
Good day!
While I was uploading the file (through FileZilla), I encountered this
message box:
[image: Inline image 1]
Will this affect uploading process?
Thank you.
<>___
Please keep all replies on the list by using "reply all"
in your mail
Hello,
I am trying to run GATK on a local galaxy installation. I get the following
error:
# ERROR
--
# ERROR A USER ERROR has occurred (version 1.5-21-g979a84a):
# ERROR The invalid arguments
Hello,
I am running a local galaxy server and tried to add the downsampling script
for SAM/BAM files from Brad Longhorst which I found on Github. It uses a
modified picard_wrapper.py. I get everything running except that the end
file shows up empty. I realised when looking at the log file that th
Peter,
I have been able to duplicate the error on nlstradamus, and hope to have
a fix out soon.
--Dave B.
On 8/1/13 07:21:17.000, Peter Cock wrote:
Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.
On Thu, Aug 1, 2013 at
Hi there,
I'm looking for an elegant way to extract the metadata for a Galaxy history
item from a PostgreSQL database. My special interest lies in the path to the
output file and the input parameters. Has by any chance anybody already done
this and a ready to use python script at hand? ;)
Than
Rodolfo,
In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu? To retrieve
the revision, execute the following command in your galaxy root directory:
hg id
To clarify, our understanding is that you installed the ncbi_bl
This bug has been fixed in our code repository and will be included in our next
release, which is due out in a couple weeks.
Best,
J.
On Aug 1, 2013, at 1:25 AM, Philipe Moncuquet wrote:
> Hi guys,
>
> Since the last update of Galaxy. We are enable to edit pages on our local
> instance. Pages
On Thu, Aug 1, 2013 at 2:58 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> The main tool shed was updated on schedule on Tuesday, July 30.
>
> As Nate stated in his reply to you regarding your question about the target
> date for the next Galaxy release, the next-stable branch was created on
> that da
Hi all
Apologies if I am in the wrong channel to post this. I have been using
Galaxy for a couple of months now and I'm still finding my way around the
mass of info
Some of the XML config file tags have a string interpolation type of
variable such as ${tool.name} in:
label="${tool.name} on ${on_
Hi Peter,
The main tool shed was updated on schedule on Tuesday, July 30.
As Nate stated in his reply to you regarding your question about the target
date for the next Galaxy release, the next-stable branch was created on that
date. The release process is such that when the next-stable branc
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo wrote:
> On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock wrote:
I've seen that kind of error from NCBI BLAST+ before - do you
know which of the BLAST tools was this, and what the query
was?
>>>
>>> The repo was:
>>> repos/devteam/ncbi
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock wrote:
> On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo wrote:
>> On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote:
>>> On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote:
People,
I successfully installed NCBI_Blast_Plus from the to
On Mon, Jul 29, 2013 at 10:27 PM, Nate Coraor wrote:
> On Jul 29, 2013, at 1:02 PM, Peter Cock wrote:
>
>> Hi all,
>>
>> Is there a target date for the next Galaxy release, or should that
>> differ, the next update to the main Tool Shed?
>
> Hi Peter,
>
> The next release is planned for August 12.
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo wrote:
> On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote:
>> On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote:
>>> People,
>>>
>>> I successfully installed NCBI_Blast_Plus from the toolshed
>>> The tool, however, failed to work giving the fo
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock wrote:
> On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote:
>> People,
>>
>> I successfully installed NCBI_Blast_Plus from the toolshed
>> The tool, however, failed to work giving the following error:
>>
>> Fatal error: Exit code 255 ()
>> Error: NC
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo wrote:
> People,
>
> I successfully installed NCBI_Blast_Plus from the toolshed
> The tool, however, failed to work giving the following error:
>
> Fatal error: Exit code 255 ()
> Error: NCBI C++ Exception:
>
> "/usr/local/galaxy/galaxy-dist/da
People,
I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:
Fatal error: Exit code 255 ()
Error: NCBI C++ Exception:
"/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.
On Thu, Aug 1, 2013 at 11:47 AM, Peter Cock wrote:
> On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock wrote:
>> On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier wrote:
>>> Peter,
>>>
>>
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier wrote:
> Peter,
>
> I've created a Trello card where you can track this issue:
> https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
>
> Most of these look like display issues, the test results are correctly
> recorded in the database
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock wrote:
> On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier wrote:
>> Peter,
>>
>> The issue with seq_rename incorrectly failing functional tests has been
>> resolved in 10266:fe04978dadac, and the test results will be corrected the
>> next time the automate
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier wrote:
> Peter,
>
> The issue with seq_rename incorrectly failing functional tests has been
> resolved in 10266:fe04978dadac, and the test results will be corrected the
> next time the automated testing framework runs. I'm still looking into the
> othe
Hi Piotr,
In our proteomics lab, a protein sample is fractionated (by e.g. pH)
before analysis in a nr of sample fractions. The fractions are then run
through the mass spectrometer one at a time. Each fraction yields a data
file.
The mass spec data is then matched to peptides by searching a
Il 2013-07-30 17:18 Peter Cock ha scritto:
Hello all,
Re:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011557.html
Something I raised during the GCC2013, and we talked about
via Twitter as well was a Galaxy environm
Hi,
I think you can get reference genomes from UCSC,and then make Bowtie2 index
data by bowtie2-build.Other way you can try rsync to get the index files ,for
more information you can see
http://wiki.galaxyproject.org/Admin/Data%20Integration .
Hope to help you.
shenwiyn
From: Gerald Bothe
D
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