Good luck,
Enis
On Thu, Apr 28, 2011 at 3:16 AM, Clare Sloggett s...@unimelb.edu.auwrote:
Hi all,
I would like to set up Galaxy locally. At the moment, I'm just trying to
use it on my desktop (a Mac, OSX 10.6.7), but later we will want a local
server to play with.
Rather than install
, 2011 at 9:14 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Clare,
On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
Hi all,
Most of our playing around with Galaxy has been in getting it working
on our local cloud, but now for the first time I'm configuring a
non-cloud local install
Hi all,
I am a little confused as to the right way to configure my installed NGS tools.
From the documentation I've found and from looking at the xml/python
wrappers, it looks to me like the NGS tool wrappers simply call the
tools and assume they will be in the galaxy account's PATH. For
Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor ja...@jamestaylor.org wrote:
On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote:
If this is the case, what is the best way to install and maintain two
versions of the same tool? I can write code
%20Setup to
save time for people like me who had tools installed in a non-standard
place.
Thanks again!
Clare
On Wed, Nov 16, 2011 at 3:01 PM, Clare Sloggett s...@unimelb.edu.au wrote:
Great! Thanks James, this is exactly what I need.
On Wed, Nov 16, 2011 at 2:20 PM, James Taylor ja
or would it be better just to
raise an issue?
Thanks,
Clare
On Wed, Nov 16, 2011 at 4:33 PM, Clare Sloggett s...@unimelb.edu.au wrote:
Looks like it's working! The problem I had run into, in hindsight, was
a) I hadn't set tool_dependency_dir as I didn't know about it
b) if I had set it, I
Hi Jeremy, Enis,
That makes sense. I know I can configure how many threads BWA uses in
its wrapper, with bwa -t. But, is there somewhere that I need to tell
Galaxy the corresponding information, ie that this command-line task
will make use of up to 4 cores?
Or, does this imply that there is
Hi galaxy-devs,
Quick question: when using the cloud console on CloudMan, it's
possible to add different types of nodes (large, micro, etc) to the
virtual cluster using the 'Add Nodes' option at the top. I can also
remove a given number of nodes using the 'Remove Nodes' option at the
top.
is being run (BWA), but if analyses are being run
that use multiple tools, jobs will get spread over the cluster to balance
the overal load a bit better than by simply looking at the number of slots.
Enis
On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett s...@unimelb.edu.au wrote:
Hi Jeremy
/2011-10-19--03-14
You simply paste that string into new cluster box you mentioned.
Enis
On Thu, Dec 1, 2011 at 6:31 AM, Clare Sloggett s...@unimelb.edu.au wrote:
Hi Enis, Jeremy, and all,
Thanks so much for all your help. I have another question which I
suspect is just me missing something
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne
.
Any thoughts?
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854
is all that's needed?
Clare
On 18 June 2012 19:50, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jun 18, 2012 at 10:29 AM, Clare Sloggett s...@unimelb.edu.au wrote:
Hi all,
I'd like to suggest, or request, a feature - I think that posting to
galaxy-dev is the right place to start
On 1 August 2012 15:28, Clare Sloggett s...@unimelb.edu.au wrote:
I can run
galaxy-dist without problems and have been working with that (so its
eggs are all installed already), but now I want to create a pull
request so want to run galaxy-dist.
oops, of course I mean 'so want to run galaxy
more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Any idea what is causing this?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life
on galaxy.
Works fine after that for me.
Cheers
Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett s...@unimelb.edu.au
wrote:
Hi Scott,
Thanks very much for this!
virtualenv is ok I think:
clare$ echo $PATH
/Users/clare/galaxy/galaxy_central_env/bin: .
which is where I
the problem. I think it might be due to an erroneous
version of the egg hosted on galaxy.
Works fine after that for me.
Cheers
Tomithy
On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett s...@unimelb.edu.au wrote:
Hi Scott,
Thanks very much for this!
virtualenv is ok I think:
clare$ echo
reference genome
field is not. The type of the reference genome field also presumably
depends on which value is supplied for the referenceGenomeSource
conditional.
Is there currently a way to specify (or see) these missing fields?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
supported.
As always, community contributions are welcome and encouraged.
Best,
J.
On Aug 23, 2012, at 4:10 AM, Clare Sloggett wrote:
Hi guys,
The Tools API is currently working for me from galaxy-central, but I'm
not sure how to correctly run a tool. Are there any example scripts
/
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
Dataset is connected to?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357
.
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
)
Module elementtree.ElementTree:859 in parse
Module elementtree.ElementTree:576 in parse
TypeError: coercing to Unicode: need string or buffer, NoneType found
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation
,
status='Uninstalled', error_message=Null where name = 'bcftools_view';
Thanks very much! Yes it's postgres. I'll let you know if I succeed.
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University
.
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
with this?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854
exported Workflow was built with, and I'm not
sure how to do it without confusing them.
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street
Oops sorry, meant to keep the list cc'd - resending.
On 18 March 2013 16:18, Clare Sloggett s...@unimelb.edu.au wrote:
Hi Rob,
Were you using a very old version of the library and examples or was it
quite recent? In any case, try grabbing the script from
https://github.com/afgane/bioblend
. Is it necessary for it to be this way, or are they just
there for historical reasons?
If it would be desirable to either only have one show-dataset REST method
or to make the behaviour of the two identical, should I add a Trello card
for this?
Thanks,
Clare
--
Clare Sloggett
Research Fellow
one of very few users of this instance (quite likely the only user
right this moment). I don't think the server is busy, so I'm not sure why
the files uploads don't seem to be proceeding. How can I investigate
further?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life
Sorry, missed some information: there are a handful of files, 35MB
(gzipped) each. The issue occurs even if I only try to upload one of them
though. The server is a 16-core machine.
On 21 August 2013 17:08, Clare Sloggett s...@unimelb.edu.au wrote:
Hi,
I am having trouble uploading files
:
Hi Clare
a few points to start:
- do you define the 'File Format'?
(don't use 'Auto-detect' for big files)
- and similar to a recent question on the list: check your proxy
settings
Regards, Hans-Rudof
On 08/21/2013 09:09 AM, Clare Sloggett wrote:
Sorry, missed some
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