:)
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Duddy, John wrote:
The sample tracking system looks interesting. It looks like this is designed
to have the sequencers modeled in Galaxy, have Galaxy pull the data from the
sequencers, and might assume 1-1 pairing between sequencing run and samples.
I'd like to be able to support pushing
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On Wed, Jun 1, 2011 at 3:34 PM, Nate Coraor n...@bx.psu.edu wrote:
Jean-Baptiste Denis wrote:
My goal is to delagate the management of library/datasets to a galaxy
admin of each team from the beginning : i do NOT want a SINGLE
independant super admin to manage the access for multiple team, it
(), exec_before_process(), exec_after_process() it doesn't
change the dataset name even after refreshing my history.
Has anyone had success setting dataset label/name and other attributes using
one of the custom code hook functions??
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Thanks - code to accompany good suggestions is always appreciated :)
I'll write a test and get a patched version on test as soon as I get
some time - travelling all day today - will let you know when it's
done
On Fri, Jul 1, 2011 at 7:20 AM, Assaf Gordon gor...@cshl.edu wrote:
Hello Ross
FYI: I patched the wrapper to offer all the weblogo Y axis scale
options and an additional test to central #5766 and some additional
dependency error reporting in #5772 - latest wrapper version is 0.4
On Fri, Jul 1, 2011 at 8:28 AM, Ross ross.laza...@gmail.com wrote:
Thanks - code
to upload the file again, but change the
filename? I just wonder if that original file didn't get cleared out.
Alison
-Original Message-
From: Ross [mailto:ross.laza...@gmail.com]
Sent: Monday, July 18, 2011 8:51 AM
To: Alison Harrill
Subject: Re: [galaxy-bugs] Error message when trying
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On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom -
to change the output dataset name based
on some logic - but if the boolean works, I'd recommend moving on :)
On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked
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Nikhil,
You've found an old wart - try using extra_files_path
I don't remember exactly why but it's write to files_path but read
from extra_files_path
:0
On Fri, Sep 2, 2011 at 9:21 AM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi all,
So I am writing XML files for an analysis pipeline. The
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wrote:
Hi Ross,
Yes, I did try that... but what I want is string parameter that
changes
based on whether or not you've checked a checkbox (or a way to change
the
label of the output based on whether or not the checkbox was checked).
So
my idea below did work, but it seems like a hack
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On Sun, Sep 25, 2011 at 9:33 PM, Antonio Ribeiro acbello...@gmail.com wrote:
Hi Ross and Matthew,
I'm a newbie to Galaxy and got the same error while trying to process some
Illumina data... Thanks for your posting and tips!
So, just to confirm the understanding: when installing a local instance
:04 AM, Ross ross.laza...@gmail.com wrote:
Michael,
Thanks for pointing these warning errors out. I think they're harmless
and can be ignored but I'll definitely take a look later today and
check in a fix.
As I recall, we had some discussion some months ago about whether to
allow the user
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Hi, Stefanie.
I think you might want a URL pointing to an archived history if you
want to move your history to a different Galaxy?
I imported your test history into my account on main, then I used the
'export to file' option (it might not be optimally named since it
really creates an importable
an import
job that never finishes?
On Tue, Oct 25, 2011 at 9:02 PM, Stefanie Ververs
stefanie.verv...@fh-stralsund.de wrote:
Hi Ross,
that is exactly what I tried - Export to file and then enter the link into
Import from File.
But the History never appears in the account on our Galaxy
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, metadata may
need tweaking after the upload - which is why artifacts likely needed
downstream are best written as separate history items with metadata
correctly set.
On Tue, Nov 1, 2011 at 11:03 AM, Jesse Erdmann jerdm...@umn.edu wrote:
On Tue, Nov 1, 2011 at 9:07 AM, Ross ross.laza...@gmail.com
Hi James,
Existing tools mostly take file paths. This has arguably useful side
effects in isolating cluster node execution from the galaxy server
process and persisting the computation input on a file-system -
arguably more stable long term than queries on dynamic database tables
- and maybe not
Hi Ivan,
In particular the data which I'm trying to upload are
created with rexpression (incidentally, is it still
supported or novel versions are attended?), because
Unfortunately, rexpression is not supported at present- the source is
readily available from bitbucket but the original author
Please ignore this message unless you maintain a local Galaxy instance and
use FastQC.
The most recent FastQC release 0.10.0 fixes some bugs but also completely
changes the HTML layout of the report in ways that break the old wrapper.
I've updated the wrapper script and tests to cope with this,
...
On Fri, Nov 18, 2011 at 10:50 AM, Paniagua, Eric epani...@cshl.edu wrote:
Hi Ross,
That's excellent, thanks for jumping in!
I've been charged with constructing a Galaxy tool kit for basic microarray
data analysis for my group's Galaxy instance, and I looked at your Rgenetics
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Hi, L-A,
2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de:
Hi Ross
Thanks a million, I hg-pull'ed it solved the problem!! Please push it to
galaxy-dist? ;)
Glad to hear it works - thanks for reporting back.
I ran in another little bug though, but nothing serious, you might
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http://www.biodalliance.org/index.html
embeddable - DAS native, but local server bigBed/bigWig files
http://www.biodalliance.org/bin.html can be served.
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, including the outputs in
workflows when their number is not known at execution may be tricky, but at
least this is a generic approach and won't require any changes to any of
the tools that generate Html outputs?
On Tue, Feb 21, 2012 at 8:45 AM, Anthonius deBoer thondeb...@me.com wrote:
Hi Ross
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/app/lib path to the galaxy user's
path so the nodes running jobs inherit those paths because of the -V
switch.
I hope this works!
On Tue, Apr 17, 2012 at 5:10 PM, zhengqiu cai caizhq2...@yahoo.com.cn wrote:
Hi Ross,
Thank you for your reply.
I tried it, and it was still not working.
Only
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On Wed, Apr 18, 2012 at 10:50 AM, zhengqiu cai caizhq2...@yahoo.com.cn wrote:
Hi Ross,
Thank you for your reply.
It still did not work.
I think SGE knows the path of samtools. Here is a test case I added to
Galaxy, and it creates the index for fasta file. I
can.
On Wed, Apr 18, 2012 at 11:39 AM, zhengqiu cai caizhq2...@yahoo.com.cn wrote:
Hi Ross,
I did not compile samtools using the --prefix. The samtools I used comes with
Galaxy AMI image, and I copied it to the same path on my EC2. How to compile
samtools using --prefix? I just typed 'make
that
there are many more Galaxy installations in that part of the world (and you
have Enis and Ross in Australia now). Would this be a good opportunity to
set up the first (to my knowledge) regional user group? If anyone thinks
this is a good idea, please respond (and create a new thread).
Finally, Ann
Hi, Ciara,
AFAIK new tools always require a server restart at present, but an
already loaded tool can have updates to the tool XML re-read using the
'Reload a tool's configuration' option from the administrative menu if
your login is listed as an administrator in the config file.
Restarting
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Thanks again for your help!
Dan
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So is there any specified thing to do to recover the component files of a
composite file ?
Best regards,
Marine
--
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*À :* Marine Rohmer marine.roh...@yahoo.fr
*Envoyé le :* Mercredi 13 juin 2012 10h50
*Objet :* Re
how to fix it either...
Any ideas ?
Thank you for your attention,
Marine
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Hi, Thon
I'm guessing here: but now that bwa is kept in the toolshed, the tool name
appears to be
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according
to your job runner entry - so I wonder if that whole ugly string now needs
to be in the tool_runners section to over-ride
Alex, xvfb http://www.xfree86.org/4.0.1/Xvfb.1.html works for our headless
node R graphics and possibly other packages.
I seem to remember writing a wiki entry but a search didn't find it...
I see someone on the dev list found the toolfactory code which does a lot
of sensible things automatically
I'm sure you checked carefully before posting, but your traceback ends
with KeyError:
'thype' suggesting maybe a simple syntax/spelling problem to me.
On Sat, Dec 29, 2012 at 7:36 PM, Tan Jun tanjun2...@gmail.com wrote:
**
Hi, all
I'm new here.
These days I'm trying to add a tool in Galaxy,
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, 2013 at 10:58 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:51 PM, Ross ross.laza...@gmail.com wrote:
Hi, Dan.
Using format=rda will restrict the list to history items of the 'rda'
datatype - but ONLY if the rda datatype has been defined!
The easiest way to do
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
Luobin - one additional minor observation: In reality, Galaxy does not do
the displaying - it just sends stuff to the users' web browser for display.
So even when Galaxy knows what mimetype to attach to a specific image file,
the users' web browser response to that mimetype will always remain the
Neil,
If by 'multiple' you mean 'independent' galaxy instances, they must each
talk to independent backend databases, so if you're thinking of running eg
2 or more independent instances at CSIRO, each for specific tool sets and
sending each of your users to one or other of them based on some
separated or very bad things will happen.
On Fri, Feb 8, 2013 at 2:20 PM, neil.burd...@csiro.au wrote:
Thanks Ross.
** **
I did mean separate Galaxy instances like test and main with their own
independent backend databases.
** **
How could I run say a test and a main from
Hi Russell,
There may be a better way, but this works for me in the Toolfactory to
create space and special character free names?
param name=foo type=text value= label=Foo
sanitizer invalid_char=
valid initial=string.letters,string.digits/
/sanitizer
/param
On Wed, Feb 13, 2013 at 11:22 AM,
I don't think there's one in a toolshed but someone's clearly done some
work on it at http://galaxy.cbiit.cuhk.edu.hk/
Perhaps you may be able to convince them of the many benefits of
contributing back to the community by sharing some of their tool code?
On Wed, Feb 13, 2013 at 12:32 PM, Jorge
Hello, Min
This tool has been stable for a while now and that variable cl is defined
as a list in line 52 just above line 63, so this error seems very strange
unless you made changes to the source code?
It's hard to know where to start helping because there are lots of useful
pieces of
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See if adding the default queue name to the job runner path - eg:
default_cluster_job_runner = drmaa:///default
works any better?
Galaxy will default to the local runner if it can't find the nominated
drmaa path AFAIK and I don't think 'default' is the default
:)
On Tue, Feb 26, 2013 at 4:51
Hi, shenwiyn
I'd also add:
Fourth, replace distributed default sqlite with postgresql
to your list if it's for any serious use. Sqlite is ok for testing.
On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote:
**
**Hello Carl,
Thank you very much for your help.I have some
Hi, Charles,
builds.txt is what tells the Galaxy framework about available genomes.
Various binary index files created from those genomes are separately
managed for specific tools since some folks won't need some application
specific sets of indexes for any given genome - so you need to edit a
Hi, David.
does enclosing your XML in a CDATA section help? It should just get written
out without being interpreted, and it works for me in the toolfactory - the
contents still get written out but without the CDATA section.
configfiles
configfile name=loadTestxml
![CDATA[
*!DOCTYPE crystal
Neil,
AFAIK, python will not load a module unless the relevant script file is
marked as executable by the current user?
Try something like:
chmod ugo+x scripts/db_shell.py
and see if that fixes your problem?
On Tue, Apr 30, 2013 at 11:50 AM, neil.burd...@csiro.au wrote:
Hi,
I'm trying to
Funny, it works for me.
One last thought: You do still have the distributed __init__.py readable by
your userid in /scripts so the module loader knows it's a python package
directory?
On Tue, Apr 30, 2013 at 12:05 PM, neil.burd...@csiro.au wrote:
Thanks for the info Ross
** **
But I
Buildbot can be triggered here
http://buildbot.g2.bx.psu.edu/builders/central-py2.7-linux-x86_64-postgres
manually
I think.
On Fri, May 10, 2013 at 10:56 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Is there a more optimal time to initiate this testing process to better
accommodate those in
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-- Forwarded message --
From: מירב . mer...@gmail.com
Date: Wed, May 29, 2013 at 8:40 PM
Subject: Re: [galaxy-dev] installing galaxy
To: Ross ross.laza...@gmail.com
It worked!! Thank you very mach [?]
Merav
2013/5/29 Ross ross.laza...@gmail.com
Hi, Merav.
A fully functional
Hi, Saket.
Welcome aboard - help is always available here or irc if you're in the
right timezone.
https://chgr.mc.vanderbilt.edu/plato/https://chgr.mc.vanderbilt.edu/plato/steps/3
is
a brand new eQTL option from Marylyn Ritchie's group I stumbled across at
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Hi Saket
If you want to redirect the executable's stdout to a new Galaxy dataset
you've defined as $output, something like:
gt; '$output'
is a workable idiom for a command line AFAIK - you need to escape the
redirection '' character or you'll confuse the xml parser.
It's often possible to hack a
?
AFAIK they need to be from the same subjects - so probably need some
thought to make it optimal for a biologist user
On Tue, Jun 4, 2013 at 8:39 PM, Saket Choudhary sake...@gmail.com wrote:
Thanks Ross and Peter. That worked.
I think I will keep the Python wrapper though, gives me more
Hi Jens, the toolfactory (install from the admin menu - it's in the main
toolshed) allows admin users to paste and run arbitrary R scripts.
Yes, there are serious security issues exposing unrestricted scripting! So
the toolfactory only works for admin users and should never be installed on
Shashi,
Hans made a brave guess based on your vague question, but you'll probably
get better answers if you do us all a favour and make an effort to provide
unambiguous detail about exactly what you want to achieve.
If there is a working Galaxy tool that does what you need but using a
different
you hack
the tool into Galaxy itself or something. There is no documentation for
that.
On Wed, Jun 19, 2013 at 9:01 PM, shashi shekhar me_shash...@yahoo.co.inwrote:
Hi Ross,
thanks for the reply . actually i want to use TreeView as visulaization
tool.
TreeView X is an open source and multi
Shashi,
Beats me. Cloning the visualisation code would be a good start I'd
guess. It will not be trivial.
Others may have better ideas.
On Wed, Jun 19, 2013 at 9:56 PM, shashi shekhar me_shash...@yahoo.co.inwrote:
Hi Ross,
Actually i have to add the visualization which will be interactive
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Hi, Amanda,
If your previous version was very old, it may have lacked a parameter added
to universe_wsgi.ini some time ago to control universal sanitization of
HTML as a security precaution on public sites. If it's not already there,
could you try adding
sanitize_all_html = False
to your
Did you try what was suggested below in my reply 5 days ago?
Ross ross.laza...@gmail.com
Jun 29 (5 days ago)
to *azuzolo*, galaxy-dev
Hi, Amanda,
If your previous version was very old, it may have lacked a parameter added
to universe_wsgi.ini some time ago to control universal sanitization of
HTML
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about that Ross. I would try your wrapper of edgeR and would
happily report you the bug. Can you make me the link of Galaxy Test
Toolshed?
Thanks,
Sachit
On Mon, Jul 8, 2013 at 11:51 AM, Ross ross.laza...@gmail.com wrote:
(Sachit, please don't cross-post to the dev and user lists
Hi Dan,
That's old code. Updating will probably help.
Logging level just takes disk space, but just in case you haven't followed
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance
leaving
debug = True uncommented used to fill
Unicode isn't handled nicely yet AFAIK so
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in
position 23: ordinal not in range(128)
might mean a http://www.fileformat.info/info/unicode/char/2013/index.htm -
overtyping these in an ascii text editor will remove them but this is a
/
--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
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Hi Michael,
I think you will enter new ground with your tool. The closest tool that
will do something similar is Ross toolfactory, I think:
http://toolshed.g2.bx.psu.edu/view/fubar/toolfactory
For me one question is, do you really want to offer that service to
every user and is it save
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl
, 2013 at 11:25 AM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
Ross,
Thanks for the comments.
I've already made my main tool tool_shed compatible. What I'm wondering
about is what do I do with the tools that my tool creates?
Sincerely,
Michael E. Cotterell
Ph.D. Student
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