Hey,
I wanted to know if anyone else has had experience with database deadlock
when using dataset collections and running a large number of samples
through a workflow.
Traceback (most recent call last):
File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py"
do think (hope) the next release due out in a
> couple of weeks will result in a massive speed up in workflow
> scheduling - so hopefully we will be less likely to hit these
> conditions.
>
> -John
>
> On Fri, Feb 27, 2015 at 10:11 AM, Aaron Petkau
> wrote:
> > Hey,
> &
Hey,
So, I've been working on a tool which will product a new dataset collection
as output. I was following some of the instructions from
https://bitbucket.org/galaxy/galaxy-central/pull-requests/582/allow-tools-to-explicitly-produce-dataset/diff.
I managed to get the tool itself working, but whe
et
> the 15.07 release on github for the latest and greatest fixes.
>
> If that still doesn't work I would recommend trying to pair down the
> tool and workflow to build a minimal example to post. This really
> should work in the abstract.
>
> -John
>
> On Fri, Aug
ltering
> empty/bad datasets, zipping and unzipping pairs, splitting/merging
> using operations defined on datatypes, etc I plan to throw
> together a framework for collection operations (hopefully this next
> release cycle).
>
> -John
>
> On Fr
Hey everyone,
So I rely a lot on specific versions of tools in the toolshed, and am often
testing out the install process to make sure everything's working. Today I
noticed that my install process was failing, and it looks like it's due to
not being able to install previous versions of tools thro
t;
> This only affects devteam repos.
> We are working on a fix, please bare with us.
>
> Thank you for using Galaxy!
>
> Martin
>
> On Wed, Aug 12, 2015 at 5:44 PM Aaron Petkau
> wrote:
>
>> Hey everyone,
>>
>> So I rely a lot on specific v
; Please let us know if you find any more problems.
>
> Thank you for using Galaxy.
>
> Martin
>
> On Wed, Aug 12, 2015 at 7:21 PM Aaron Petkau
> wrote:
>
>> Heh, always something that's discovered after the fact. Happens to me
>> all the time. Thanks for g
Hello,
I'm running into some issues with maintaining multiple installable
revisions for a repository suite and I'm not sure if there's something I've
missed.
I have a local toolshed where I'm maintaining my tools, and I have a
repository suite definition, defining a number of dependencies. So, I
ttp://usegalaxy.org
>
>
> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>
>> Hello,
>>
>> I'm running into some issues with maintaining multiple installable
>> revisions for a repository suite and I'm not sure if there's something
>> I've mis
e exact revision of the tool (fasta_clipping_histogram
> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
> suite_fastx_toolkit_0_0_9 repositories which will install the requested
> versions of the tools.
>
> M.
>
> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petka
gt;>
>>> Hi Aaron,
>>>
>>> we touched this recently here:
>>> https://github.com/galaxyproject/tools-devteam/pull/267
>>>
>>> I believe that if you specify the repository_dependencies.xml of your
>>> suite in the following way:
>>>
>>>
Thanks for including me Damion.For symlinking, you're right John and I never thought about any of the issues with deleting datasets in Galaxy afterwards.The ability to define a connection for passing/failing a subsequent tool you mentioned sounds exactly what we were trying to accomplish. Is there
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