Hi all,
Is it possible to read id's from a column of an input dataset and
create a checkbox parameter with the unique id's of that column within
the same tool?
The only remotely similar action that I found is on the sorting tool
where it reads the number of the columns of that dataset and
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I want to use is genome.
conditional name=bedgraph
param name=check type=select label=Produce BedGraph
output help=Can be displayed directly on UCSC browser. One file
, since you’re
only setting the dbkey under certain circumstances.
Thanks for using Galaxy,
Dan
On Oct 15, 2014, at 6:37 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi all,
I'm trying to set the dbkey of an output file from the value (text) of
a parameter.
The parameter I
Yes!
Thank you very much Daniel.
On 15 October 2014 18:14, Daniel Blankenberg d...@bx.psu.edu wrote:
Does removing the ‘param_attribute=“value' attribute help?
On Oct 15, 2014, at 11:23 AM, Nikos Sidiropoulos nikos.sid...@gmail.com
wrote:
Hi Daniel,
Thanks for the response.
I've
Hi all,
In a tool that I am writting I want to pass an input parameter value
(string) into the output file's metadata. Meaning that one of the tool
parameters is a barcode signature, 'NNWTGXN' for example. I want that
attribute to be stored somehow in the output file in order to be read by a
Hi all,
after the latest galaxy update I've experienced the following error while
trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs ERROR 2014-06-04 14:34:56,047 One of Galaxy's managed eggs
AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi all,
after the latest galaxy update I've experienced the following error
while trying to start the server.
galaxy.eggs DEBUG 2014-06-04 14:34:56,027 Fetched
http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg
galaxy.eggs
Hi all,
a similar error with this one (
http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html)
has appeared in Galaxy reports after the last update.
It also occurs only when I'm trying to view the completed jobs in a certain
day.
Thanks in advance.
Bests,
Nikos
False alarm, the error went away when I restated the webapp.
2014-04-24 15:36 GMT+02:00 Nikos Sidiropoulos nikos.sid...@gmail.com:
Hi all,
a similar error with this one (
http://osdir.com/ml/galaxy-development-source-control/2014-02/msg00095.html)
has appeared in Galaxy reports after
Nikos,
Thank you so much for your report. This issue should be fixed now. Please
update your revision and try again.
Thanks,
Sam
On Thu, Feb 13, 2014 at 7:52 AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi all,
after the February 2014 galaxy update I'm experiencing errors
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's format
(bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests,
Nikos
/3691fd3e12ef8160ae993cef5ebd51ddeee95da1
Martin
On Fri, Feb 14, 2014 at 1:28 PM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi Sam,
thank you for the quick reply but I can't seem to find the revision, or
maybe don't know how to pull it.
I tried to check galaxy-dist on BitBucket but couldn't find any updates
Worked.
Thanks Björn!
2014-02-14 19:41 GMT+01:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Nikos,
try $input.ext ...
Cheers,
Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's
format (bam, bed, etc) to pass it as a variable to the command.
Hi all,
I'm getting the following error whenever I'm trying to run SICER
Traceback (most recent call last):
File
/steno-internal/projects/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sicer/82a8234e03f2/sicer/sicer_wrapper.py,
line 158, in module
if __name__==__main__: __main__()
Hi all,
after the February 2014 galaxy update I'm experiencing errors in Galaxy
Reports.
It only occurs when I'm trying to see which jobs were ran at a specific
date (e.g. I can see how many jobs were ran today, but when I click on the
number to see which ones it returns the following error):
Hi all,
Although users were able to create accounts till recently, now the
following error pops up whenever someone is trying to register as a new
user after filling the fields and clicking submit.
Select the user's type and information
Is anyone familiar with this error?
Bests,
Nikos
/user/
manage_info.mako.py', line 93 in render_body
__M_writer(unicode(trans.security.encode_id( user_type_form_definition.id)))
AttributeError: 'NoneType' object has no attribute 'id'
2014/1/14 Nikos Sidiropoulos nikos.sid...@gmail.com
Hi all,
Although users were able to create accounts till
...@bx.psu.edu
Hi Nikos,
did you update your galaxy version recently? Did you use galaxy form
definitions at any time?
Martin
On Tue, Jan 14, 2014 at 8:30 AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
I found the error in the logs:
Error - type 'exceptions.AttributeError': 'NoneType
Hi again
You were right. Restarting all processes solved the problem and Bismark in
now up and running.
Bests,
Nikos
2013/9/4 Nate Coraor n...@bx.psu.edu
On Sep 4, 2013, at 10:08 AM, Nikos Sidiropoulos wrote:
Hi Nate
Yes, it is a multiprocess setup. But is it because we have more than
Hi all,
I have a couple of questions regarding a server setup dedicated on Galaxy.
The idea is to buy a 64 core 256GB RAM server. From my experience I believe
that Galaxy will be able to scale up to 64 cpu's but I would like some more
feedback on this. Also, is 4GB RAM per CPU core enough for
Peter Cock p.j.a.c...@googlemail.com
On Wed, Sep 11, 2013 at 1:03 PM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi all,
I have a couple of questions regarding a server setup dedicated on
Galaxy.
The idea is to buy a 64 core 256GB RAM server. From my experience I
believe
I'm not sure how easy it would be to setup your Galaxy to only
allow one de novo assembly at a time - which would seem a
sensible precaution given you may have multiple users (or the
same user) trying to run assemblies in parallel.
I guess I could dedicate a handler to run this specific tool
Hi all
I installed bismark from the toolshed (bgruening) with all dependencies
having been installed successfully and I generated the genomes according to
the instructions.
While trying to test the tool I got the following error.
galaxy.jobs.handler ERROR 2013-09-04 13:14:26,267 Failed to
Hi Bjørn
that does not look like a bismark error. Is it happen with other tools
as well?
No, I have only experienced it with Bismark.
Not sure, sorry. But you should migrate to the new job configuration,
better sooner than later.
I am starting to get that idea. There are jobs still running
for the tool-shed tools.
Bests,
Nikos
2013/9/4 Nate Coraor n...@bx.psu.edu
On Sep 4, 2013, at 9:17 AM, Nikos Sidiropoulos wrote:
Hi Bjørn
that does not look like a bismark error. Is it happen with other tools
as well?
No, I have only experienced it with Bismark.
Not sure, sorry
Hi all
After updating to the last stable galaxy when I'm trying to upgrade the
database I'm getting the following message:
/steno-internal/projects/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/url.py:105:
SADeprecationWarning: The SQLAlchemy PostgreSQL
it would produce a better error
message than this admittedly cryptic problem. I know it is not always
possible to upgrade, but if it is easy it is something worth
considering doing.
-John
On Tue, Jun 18, 2013 at 8:18 AM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi
We are running
Hi
We are running the latest stable distribution on our server. We want
tophat2 (along with other tools) to be executed on another machine.
LWR is setup based on the online documentation (
http://wiki.galaxyproject.org/Admin/Config/LWR,
https://lwr.readthedocs.org/en/latest/)
Bowtie2 is working
Hi everybody
Has anybody used the profile memory usage feature, and if so, what are
the benefits and the compromises of it?
I'm trying to find documentation about it, without any luck.
Thanks
Nikos
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Hi everybody
Has anybody used the profile memory usage feature, and if so, what are
the benefits and the compromises of it?
I'm trying to find documentation about it, without any luck.
Thanks
Nikos
___
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Hi
Is it possible to set an expiration date for specific user accounts?
Bests,
Nikos
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