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 wrote:
> The tag won’t be going away any time soo
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 wrote:
>
> I feel like that stdio tag is going to cause it to always pass - even
> if the exit code is not 0. Am I wrong?
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
tha
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 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 29, 2015 at 8:23
John - thanks, your configfile example should work for API key. however,
is there a cheetah substitution to pull in the server's URL?
On Wed, Apr 29, 2015 at 12:20 PM, Ben Bimber wrote:
> Hi John,
>
> Thanks. To elaborate a little more: we have a LabKey Server (web front
> end for a databa
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
Unofficial way of doing this and the workaround of using configfiles
can be found in this thread:
http://dev.list.galaxyproject.org/Simple-standard-for-API-use-of-a-global-user-key-that-all-loaded-tools-can-draw-upon-td4665659.html.
There is a Trello card outlining platform work that should be done
Hello,
I am new to galaxy. I"m trying to write a data input tool wrapper. It will
call a script that does a query, produces a list of files, and then the
plan is to use the BioBlend API to create datasets/data collections in
galaxy. In other words I am making the dataset(s) based on the contents
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 replie
On Wed, Apr 29, 2015 at 4:40 PM, Roberto Alonso CIPF 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 whatever. I
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
No it just slipped through the cracks - sorry about that. I have
commented on it now. There was a time when a couple weeks before a
first response was the norm :).
Does it belong with the bam splitting pull request - is merging useful
on its own without the other piece you are working on.
-John
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 co
The 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 times w
On Wed, Apr 29, 2015 at 6:33 AM, Simon Gladman
wrote:
> Hi dev,
>
> Now that the tagset is deprecated, how do we replace that
> functionality. For example the "get microbial data" tool runs the script
> listed in the tagset to load the list of available microbe data when
> the tool is selected.
Hi dev,
Now that the tagset is deprecated, how do we replace that
functionality. For example the "get microbial data" tool runs the script
listed in the 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 15.03.2.
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
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 Baker
> 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 Baker 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 good understanding of
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
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:
>
> W
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:
so far this, assuming you enterred:
foo
bar
produced a string like:
foo__crcn__bar__crcn__
Now, with "toolform
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
https://travis
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 wrote:
> Hi Ryan
>
> I guess you can work with filters, see:
>
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.
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
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