In that case, could anyone point me to an example of a Composite
Datatype which could accept as input an unknown number of files in an
unknown number of directories. I can't seem to understand how that would
work based on the wiki.
But maybe are we anticipating a near functionality of Galaxy.
On Wed, Jan 30, 2013 at 3:01 AM, Luobin Yang yangl...@isu.edu wrote:
Hi,
I have a 'select' tag in a tool's XML file, ... when the number of options
exceeds 20, then drop down menu of the web interface displays Click to
Select or Search ... Why the behavior changed when there are 20 options
Hi,
In the 'Admin' menu, reloading a tool's xml file does not update the
tool's interface.
Thanks for any assistance,
Joachim
--
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
Unfortunately, no.
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 01/30/2013 10:56 AM, Peter Cock wrote:
On Wed, Jan 30, 2013 at 9:54 AM, Joachim Jacob |VIB|
joachim.ja...@vib.be wrote:
I'd suggest:
1) Make your new datatype a subclass of Html - it's a subclass of composite
that contains an HTML document as the object's native display - so it can
inform users what's there.
2) When constructing these new things, pass the file_path of the Html
(composite) dataset subclass to your
Hi Joachim,
are you running more than one web-worker? In that case i think it is not
possible currently. If you use the toolshed your tools will be reloaded
automatically with each update. Maybe that is an workaround for you?
Ciao!
Bjoern
Hi,
In the 'Admin' menu, reloading a tool's xml
Ok, thanks a lot, I'll try and get back to the mailing list if other
problems seem to occur.
Pierre.
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS-UPMC
Place Georges Teissier
CS 90074
29688 Roscoff CEDEX
FRANCE
Thanks. Yes, I am running multiple webworkers. OK, nice to know what
causes this.
The toolshed option will be considered.
Joachim.
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On
Hi list,
When working to get a tool wrapper Toolshed-ready, I have explored how tool
dependencies installation works, especially the download_by_url feature.
I have summarised my understanding on the Wiki (hope this is clear and
accurate):
is causing a problem on our scheduler node. Thank-you so
much for taking the time to answer my questions.
[a.cri.dsullivan@sc01 server_logs]$ tail -f 20130130
01/30/2013 10:30:50;0100;PBS_Server;Req;;Type AuthenticateUser request
received from s.cri.gal...@crigalaxy.uchicago.edu, sock=9
01/30/2013
Hi,
I need help recovering my Galaxy Wiki password. I enter my information
and I get the message about my account existing and an email was sent,
but I never receive this email.
Thanks,
Carlos
___
Please keep all replies on the list by
I have a patch to replace the searchable select implementation with
select2 which seems to work well, but still needs comprehensive
testing. I think it may address this problem. If anyone is interested
in trying it:
On Tue, Jan 29, 2013 at 11:44 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Presumably at this point changing the name in the code would
break too many things?
Actually, changing the package name would probably be a pretty clean
refactoring, just some changes in buildapp. But given how many
You may want to be careful with this solution because it allows script
injection, any HTML including javascript in the uploaded tabular file
will be executed by the .html call, with complete access to everything
in the Galaxy browser window (like your session cookies).
--
James Taylor, Assistant
Not currently, however we are planning to implement this in the future.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Sun, Jan 27, 2013 at 10:20 AM, Hagai Cohen hag...@cs.huji.ac.il wrote:
Hi,
is it possible that when I rerun a tool it will also rerun the tools that
Can you send some additional lines of the error? The important part is
to see what part of the stack is repeating. Based on what you have it
suggests recursion in trying to do a datatype conversion. Have you
modified datatypes_conf.xml and is it possible there is a problem
there? Thanks!
--
James
Hi,
I am trying to extract my sequences from a fasta file in my galaxy account
based on
the start and end positions of a gff file.
However, this is not working here. How
do I specify that the strands I am extracting are in the fasta file in my
account in Galaxy?
Should I be using another
Hi Carlos,
There does not appear to be an email address associated with your account.
I will try to associate your account with your GMail account and let you
know (off-list) when I think that is done.
And, administrative requests like these can also be sent directly to
On Wed, Jan 30, 2013 at 10:36 AM, Carl Eberhard carlfeberh...@gmail.com wrote:
Dan,
Are you cloning from galaxy-central or galaxy-dist? Are you cloning from the
tip or a specific revision?
I installed galaxy as recommended in the docs:
hg clone https://bitbucket.org/galaxy/galaxy-dist/
Thanks for your request Peter,
I've added a Trello card for this and I'll get to it as soon as possible - the
restriction is simply a bandwidth issue as my plate is maxed out and the code
renaming work just hasn't been a high priority.
Here's the link to the trello card - I believe the plan is
On Wed, Jan 30, 2013 at 11:36 AM, Carl Eberhard carlfeberh...@gmail.com wrote:
Well - as long as those errors don't happen again - it may well be progress.
For the next step, can you:
1. open Galaxy in Chrome
2. Go to the settings menu (the button with three horizontal bars on the
right side
Hi,I continue to see this error in the logs,every timea jobs finishes:galaxy.objectstore CRITICAL 2013-01-30 11:42:14,161 /mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327 deleteerror [Errno 39] Directory not empty: '/mnt/ngs/analysis/svcgalaxy/DATA/job_working_directory/000/327'When
Hi Guys,
I've just updated to the latest galaxy-central and notice a problem when
trying to export workflows via the api. In
galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in
an extra tab in lines 88 and 89, the patch is below.
PATCH using hg diff
diff -r
Hey Richard,
If you could, submit a pull request to galaxy-central through bitbucket. Even
for changes this small, it really helps keep things organized and preserves the
change history.
Thanks!
Dannon
On Jan 30, 2013, at 2:54 PM, Richard Park rp...@bu.edu wrote:
Hi Guys,
I've just
Hi Dannon,
Thanks for the help again, I just forked galaxy-central, committed the
patch, and submitted the pull request.
https://bitbucket.org/galaxy/galaxy-central/pull-request/114/fixed-error-when-retrieving-workflows-via/diff
Let me know if you need anything else,
thanks,
Richard
On Wed,
Perfect, thanks! I've merged the changes.
-Dannon
On Jan 30, 2013, at 3:55 PM, Richard Park rp...@bu.edu wrote:
Hi Dannon,
Thanks for the help again, I just forked galaxy-central, committed the patch,
and submitted the pull request.
Hi,I am trying to use the API with my galaxy server running behind a proxy server.How do I pass username/password information to the API so it can actually run?If I use the regular API calls I get a access denied...ThanksThon
___
Please keep
Hi,
I just installed Galaxy in local Centos Vm. I did my best to get everything
working ( I think). I followed the instructions in this Wiki
(http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference
genomes for the tools Bwa and Bowtie. Here is what I did in details:
I've got fix for this, add the following line between line 690 and line 691
in lib/galaxy/webapps/galaxy/controllers/admin.py :
emails.sort()
Thanks,
Luobin
On Tue, Jan 29, 2013 at 5:05 PM, Luobin Yang yangl...@isu.edu wrote:
Hi,
The list of users is not sorted when I try to impersonate a
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