Hi all,
I think this is the second time I've have the following error on
TravisCI (last time I reran a similar failure, and it worked). I've
not yet re-run the test so that you can see the full error log:
UnmappedClassError: Class 'kombu.transport.sqlalchemy.Message' is not mapped
Hi Ryan
I guess you can work with filters, see:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cdata.3E_tag_set
Regards, Hans-Rudolf
On 04/28/2015 06:28 PM, Ryan G wrote:
Hi - I'm implementing a new tool in Galaxy. The tool either takes 1 or
2 fastq files as input. If 1
Yes, for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml
Peter
On Wed, Apr 29, 2015 at 8:23 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Ryan
I guess you can work with filters, see:
Hi all
We just need some confirmation before we fix our tools:
We have several local tools, where the input is a list of (gene)names
with the following xml syntax:
param name=genenames type=text area=true size=5x20 label=gene
names help=(one per line)/
so far this, assuming you
No need, unless it becomes particularly worse after the next attempt to fix
it :)
On Wed, Apr 29, 2015 at 8:30 AM Peter Cock p.j.a.c...@googlemail.com
wrote:
Thanks Dannon,
Do you want me to send you any future TravisCI cases of this failure?
Peter
On Wed, Apr 29, 2015 at 1:14 PM, Dannon
Hi,
I have a related question, does the text-area sanitization differentiate
between the different newline formats?
Hans-Rudolf can this be your problem?
Ciao,
Bjoern
Am 29.04.2015 um 13:55 schrieb Hans-Rudolf Hotz:
Hi all
We just need some confirmation before we fix our tools:
We
Hi Peter,
No need to rerun for my benefit -- it's definitely a race condition that I
know about and think I have a fairly good understanding of now. We've
tried a few different ideas for fixing it, (obviously none of which have
worked, yet), and I've been poking at a new fix this week.
-Dannon
Thanks Dannon,
Do you want me to send you any future TravisCI cases of this failure?
Peter
On Wed, Apr 29, 2015 at 1:14 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hi Peter,
No need to rerun for my benefit -- it's definitely a race condition that I
know about and think I have a fairly
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF ralo...@cipf.es wrote:
Ok, no problems ;)
It is another PR, I think it is useful without the other PR, for example
when you map with BWA. The last PR will be like the next step, I mean for
example that you split a bam to do some calling or
Ok, no problems ;)
It is another PR, I think it is useful without the other PR, for example
when you map with BWA. The last PR will be like the next step, I mean for
example that you split a bam to do some calling or whatever. I think both
PR can live independently and together... I don't know if
Hello,
I had a quick question about how one of the cleanup scripts works.
I was wondering if admin_cleanup_datasets.py will delete old datasets even if
they have been shared or published.
Thanks for the help
-Liam
___
Please keep all
Hi John,
Thanks. To elaborate a little more: we have a LabKey Server (web front end
for a database) that manages raw files and metadata. The idea is to make a
galaxy tool where a user could do thing like query for all genomes from
males patients, age x-y, etc. I can use LabKey's APIs to return
Yes it took some experimenting but I finally figured it out.
Sent from my iPhone
On Apr 29, 2015, at 4:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Yes, for example:
https://github.com/peterjc/pico_galaxy/blob/master/tools/seq_filter_by_id/seq_filter_by_id.xml
Peter
On Wed, Apr
We have 4 different people in our sequencing lab each working on different
projects. Once sequencing is done, they want to be able to create a data
library specific for that project. Giving them all admin rights is not
what we want, but instead giving them the ability to add data libraries so
Hi dev,
Now that the code tagset is deprecated, how do we replace that
functionality. For example the get microbial data tool runs the script
listed in the code tagset to load the list of available microbe data when
the tool is selected. This doesn't seem to work in the latest stable
15.03.1 or
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman
simon.glad...@unimelb.edu.au wrote:
Hi dev,
Now that the code tagset is deprecated, how do we replace that
functionality. For example the get microbial data tool runs the script
listed in the code tagset to load the list of available microbe data
You are correct. It's always passing even when it fails. There was nothing in
the docs to indicate a pass.
Sent from my iPhone
On Apr 28, 2015, at 3:44 PM, John Chilton jmchil...@gmail.com wrote:
I feel like that stdio tag is going to cause it to always pass - even
if the exit code is
Hi Dan,
Thanks for the reply and the suggestions. I think the data libraries would
work much better than the get_microbial_data tool as then it would be more
easily kept up to date.
Cheers,
Simon.
On 30 April 2015 at 01:01, Daniel Blankenberg d...@bx.psu.edu wrote:
The code tag won’t be
Hello,
I created a PR https://github.com/galaxyproject/galaxy/pull/149 dome days
ago, but I don't have any feedback yet, is there any problem with it? Is it
not interesting for the current Galaxy? didn't the authors realized about
it? It would be nice to have some feedback, even if it is not a
The code tag won’t be going away any time soon, but in many cases there are
other ways to do what this tag does, using the built-in dynamic options (in
particular, currently for tab-delimited files), that are much preferred. So it
is deprecated, and it should be used sparingly, but there are
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