Hi again,
Has anyone had time to look into the traceback?
Best,
Martin
From: martinchristianse...@hotmail.com
To: jmchil...@gmail.com; n...@bx.psu.edu
Date: Tue, 12 Aug 2014 15:59:53 +0200
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'
Hi guys,
Thanks for
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
I'm working on composite datatypes now (for PacBio SMRT cells). In the
datatype I know I'll have files with variable names (e.g. .1, .2, .3) and
after using the blast datattype as reference material, I noticed
On Mon, Jul 28, 2014 at 9:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try to
Hello All,
I have a little issue. I want create workflow with loop but workflow's
nodes must use different settings in each loop steps.How can i do this?
___
Please keep all replies on the list by using reply all
in your mail client. To
It's currently not possible to build loops into galaxy workflows. Major
workflow engine enhancements are being worked on, but for an immediate
solution you could drive something like this using the API if you wanted to.
-Dannon
On Thu, Aug 14, 2014 at 8:54 AM, Görkem Erdoğan
Dear UK Galaxy-devs,
We're delighted to announce the launch of the UK Galaxy Community.
Please visit the site and have a look around:
http://galaxy-community.org.uk/
The aims of Galaxy-UK are:
* To bring the Galaxy community in the United Kingdom closer together
* Identify and address
Amazing!
All the best from Germany!
Bjoern
2014-08-14 15:21 GMT+02:00 graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.uk:
Dear UK Galaxy-devs,
We're delighted to announce the launch of the UK Galaxy Community.
Please visit the site and have a look around:
Not to say 'exemplary' - really great :).
@Björn: phone call within the next days?
Cheers,
Sebastian
bjoern.gruen...@googlemail.com schrieb:
Amazing!
All the best from Germany!
Bjoern
2014-08-14 15:21 GMT+02:00 graham etherington (TSL)
graham.ethering...@sainsbury-laboratory.ac.uk
I'm all in! :)
2014-08-14 17:11 GMT+02:00 Sebastian Schaaf sch...@ibe.med.uni-muenchen.de
:
Not to say 'exemplary' - really great :).
@Björn: phone call within the next days?
Cheers,
Sebastian
bjoern.gruen...@googlemail.com schrieb:
Amazing!
All the best from Germany!
Bjoern
14.08.2014, 10:01, "Peter Cock" p.j.a.c...@googlemail.com:On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using
Hi Team,
I have installed a fresh version of Galaxy and am having an issue with the
'Upload File' tool. When I attempt to use it it just sits and spins. No data
gets uploaded. I have looked through the universe.wsgi.ini file and cannot
find anything there that stands out. Can you point me
No sure if this will help but you may want to check this. We just fixed a
problem from uploading small files via the ftp directory. Our nfs mount was set
to cache file meta data about every 30 sec. This proved problematic when
uploading a small fasta file that previously uploaded. Every time
Hi Jim
Try setting it like this:
default_cluster_job_runner = drmaa://-w n -l mem_free=16G/
I've just tried it and worked fine.
Sorry for a delay in getting back to you,
Enis
On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com
wrote:
I have a galaxy/cloudman cluster where
thanks, I ended up doing subinvocations (submitting a job from within a
job) because one tool in particular needs lots of memory. Is there a way to
set these things on a per-tool basis (which would let me remove the
subinvocation)?
Jim
On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan
Hello everyone,
We are considering to disable the deprecated upload tool form which is
currently accessible through Tool panel Get Data Upload file. The new
upload feature (icon at the top of the Tool panel) covers all of its
functionality except uploading composite datatypes like e.g. Velvet.
If I'm understanding your question correctly (ie, have the ability to
specify SGE requirements on a per-tool basis), then yes. You'd do something
like this in universe_wsgi.ini:
[galaxy:tool_runners]
bwa_wrapper = drmaa://-pe smp 2/
bowtie2 = drmaa://-pe smp 2/
On Thu, Aug 14, 2014 at 2:26 PM,
Perfect, thanks! That's in addition to the default arguments?
On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan afg...@gmail.com wrote:
If I'm understanding your question correctly (ie, have the ability to
specify SGE requirements on a per-tool basis), then yes. You'd do something
like this in
The default args will apply to all the tools. Tool-specific args will apply
only for the tool you specify and those overwrite the default (ie,
arguments will not add up).
On Thu, Aug 14, 2014 at 2:53 PM, Jim McCusker jmccus...@5amsolutions.com
wrote:
Perfect, thanks! That's in addition to the
So far I have been trying to avoid this, but I would like to see
packaged pycurl on the toolshed now.
This is where my package sits:
https://testtoolshed.g2.bx.psu.edu/repository?repository_id=534efefdbab02103
and this is the error:
Traceback (most recent call last): File setup.py, line 563, in
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