Hi,
when I start a lastz job it submits a job to GridEngine. But this job seems to
hang.
The process running is
python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source=
...
This wrapper seems to not start a lastz but lastz is in the path.
After 2 days then Galaxy shows
Hi Joachim,
By the way: do you know what the reason is for this setting? Is there a known
security problem that triggered this feature? If you add only trusted tools to
your Galaxy environment, then this is not needed, right?
This change was mentioned briefly in March 12, 2012 Galaxy
I have no clue at all, sorry.
Cheers,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 11/15/2012 09:14 AM, Lukasse, Pieter wrote:
Hi Joachim,
By the way: do you know what
Can anyone give some more information about this?
Thanks,
Pieter.
-Original Message-
From: Joachim Jacob [mailto:joachim.ja...@vib.be]
Sent: donderdag 15 november 2012 9:17
To: Lukasse, Pieter
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Display of HTML type broken in new
On Thursday, November 15, 2012, Lukasse, Pieter wrote:
Hi Joachim,
By the way: do you know what the reason is for this setting? Is there a
known security problem that triggered this feature? If you add only trusted
tools to your Galaxy environment, then this is not needed, right?
This
It's part of Galaxy security against XSS attack by sanitizing html.
If you trust your users you don't need it. If you run a public server, it's
your call.
On Thu, Nov 15, 2012 at 7:19 PM, Lukasse, Pieter pieter.luka...@wur.nlwrote:
Can anyone give some more information about this?
Thanks,
Good suggestion. Then the sanitisation should be switched off by
defining a parameter in the tool outputs section if your data is html.
Joachim
On 11/15/2012 09:28 AM, Peter Cock wrote:
On Thursday, November 15, 2012, Lukasse, Pieter wrote:
Hi Joachim,
By the way: do you know what
Dear devs,
How will the scatterplot in the future be integrated in Galaxy, e.g, for
saving and displaying a scatterplot in pages?
Kind regards
Joachim
--
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
Hi all,
Is this likely to cause problems using Galaxy on SQLite (the default and very
handy for a development machine)?:
$ sh manage_db.sh upgrade
107 - 108...
Add the ExtendedMetadata and ExtendedMetadataIndex tables
SQLite does not support ALTER TABLE ADD FOREIGN KEY; see
Hi all,
Something has changed in the job handling, and in a bad way. On my
development machine submitting jobs to the cluster didn't seem to be
working anymore (never sent to SGE). I killed Galaxy and restarted:
Starting server in PID 12180.
serving on http://127.0.0.1:8081
On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
Something has changed in the job handling, and in a bad way. On my
development machine submitting jobs to the cluster didn't seem to be
working anymore (never sent to SGE). I killed Galaxy and restarted:
Dannon,
I wanted to apply the patch as well on our fresh instance. But it fails with
the error of uncomitted changes..
But we only pull/merge/update using hg nothing else we do with itany clues?
We only locally modified files of course (like the wsgi.ini files and loc
files).
$ hg patch
On Thu, Nov 15, 2012 at 10:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Nov 15, 2012 at 10:06 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi all,
Something has changed in the job handling, and in a bad way. On my
development machine submitting jobs to the cluster didn't
Hi,
I upgraded to the latest version and again some tools moved to tool_shed. I now need to set job
runners for these tools. Is there an easy way to get the tool_ids other then hovering the mouse over
the tool name and write down the id?
regards, Andreas
--
Andreas Kuntzagk
Hi,
I'm having some problems restarting our galaxy server after upgrading it to the
latest version today...
Here is the error message:
python path is:
/opt/local/home/webapp/galaxy/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs2.egg,
Hi Andreas,
Assuming you have executed the migration process for the tools so they are now
installed into your Galaxy instance from the tool shed, you can check the
entries in the migrated_tools_conf.xml file and get the ids. Entries will look
something like the following where you can get
A user encountered a KeyError when clicking the View Details icon from an
older Cuffdiff history item:
File '/galaxy/PRODUCTION/database/compiled_templates/show_params.mako.py', line
106 in render_body
__M_writer(unicode( inputs_recursive(tool.inputs, params_objects, depth=1) ))
File
Hi Greg,
No change at all, how can I check?
[webapp@uk-cri-lbio07 galaxy]$ hg status | grep -v '^?'
M tool-data/shared/ucsc/ucsc_build_sites.txt
The problem may be that I did not upgrade since 14 June 2012. Could it be
related to the version of tools in the database? Please advice me if you
HI Anne,
Just to confirm, you are running the latest dist release which went out
yesterday, correct? If so, perhaps you can try this:
%sh manage_tools.sh upgrade
The above will set the value of the migrate_tools.version column in your
database to the latest migration value. After doing
Hi Akshay,
Please post all technical questions directly to the galaxy-dev mailing
list. I'm sure we'll be able to help out shortly,
Jen
Galaxy team
http://wiki.galaxyproject.org/Support#Mailing_Lists
Hello,
My name is Akshay and I am a computer science graduate student at UGA in Dr.
Hi Akshay,
I don't know the answer to your question. So:
1) I went to http://galaxyproject.org/search/web/ and searched for
timeout and then timeout workflow. There are lots of email threads
(and I learned some stuff :-), but I didn't find a direct answer to your
question.
2) I'm sending your
Many thanks for the links, exectly what I need! (somehow missed to look
in the right place, obviously ...)
Best
// Samuel
On 11/14/2012 04:02 PM, Hans-Rudolf Hotz wrote:
Hi Samuel
Have you looked at Data Libraries ?
(http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries )
also look
Scatterplots will behave just as Trackster does: you'll be able to save
scatterplots and embed them in Pages.
Looking forward, the Galaxy team is in the process of developing a plug-in
framework for visualizations that will allow for arbitrary Web visualizations
to work with Galaxy. With this
Hi Greg,
Brilliant! Thanks a lot for your advice, it worked!
I do run the latest dist release that went out yesterday. Thanks again for your
prompt help, it is very much appreciated.
Cheers,
Anne.
On 15 Nov 2012, at 16:45, Greg Von Kuster g...@bx.psu.edu wrote:
HI Anne,
Just to confirm,
I'd also like to add in a way for the user to save/download the svg from
our visualizations that use it. Unfortunately, there's no
clean/straightforward way to do this. I've seen some solutions that are
better than nothing and it's on the list as well.
On Thu, Nov 15, 2012 at 2:45 PM, Jeremy
Any idea would be appreciated. I get a This link may not be followed from
within Galaxy after following these steps:
Get Data - Upload File - File Format:
Type lpe - select lped from autocomplete list.
I've compiled latest stable nginx in CentOS 6.3 with upload module
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