On Thu, Mar 13, 2014 at 6:40 PM, Sanka, Ravi wrote:
> I do not think so. Several individual datasets have been deleted (clicked
> the upper-right X on the history item box) but no History has been
> permanently deleted.
>
> Is there any indication in the database if target dataset or datasets were
On Tue, Mar 4, 2014 at 12:19 PM, Peter Cock wrote:
> On Tue, Mar 4, 2014 at 10:35 AM, Björn Grüning
> wrote:
>> Hi Peter,
>>
>>> Hello all,
>>>
>>> I've mentioned before that a forthcoming update to the BLAST+
>>> Galaxy wrappers would be adding a most customisable output
>>> option with pick-yo
Hi there,
We have installed a local copy of galaxy but there seems to be a strange
behavior with deleting data sets in the history panel. A few users complain
that they have deleted their data sets (I can confirm that) but somehow the
quota limit still doesn't show the appropriate freed space. Loo
On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze
wrote:
> Hi there,
>
> We have installed a local copy of galaxy but there seems to be a strange
> behavior with deleting data sets in the history panel. A few users complain
> that they have deleted their data sets (I can confirm that) but somehow
I don't even think you can delete datasets in workflow presently - let
alone permanently delete them - only "hide" them.
https://trello.com/c/YfLGkJKe
The core team just meet and a number of high priorities for the next 9
months were identified and reworking workflow scheduling was very high
on t
Perfect! This solved my problem.
Alex
On Fri, Mar 14, 2014 at 1:23 PM, Peter Cock wrote:
> On Fri, Mar 14, 2014 at 12:28 PM, Alexander Kurze
> wrote:
> > Hi there,
> >
> > We have installed a local copy of galaxy but there seems to be a strange
> > behavior with deleting data sets in the histo
On Fri, Mar 14, 2014 at 1:31 PM, Alexander Kurze
wrote:
> Perfect! This solved my problem.
>
> Alex
That's progress. I suspect something is going wrong in the
cleanup scripts failing to update the totals - but as a workaround
you could include set_user_disk_usage.py as part of the cleanup
cron jo
I am not sure I understand what you mean, but if you are setting the
job to run with a ppn of greater than one but GALAXY_SLOTS is being
evaluated as 1 then you have likely uncovered a bug - maybe in the
runner, your job configuration, or the GALAXY_SLOTS logic for
pbs/torque.
I have created a Gal
I did not implement this - so this is just an educated guess but I
believe the relevant line of code is this:
https://bitbucket.org/galaxy/galaxy-central/src/3fb927653301a0c06a0bf94f2b6bd71b3595ec0d/lib/galaxy/objectstore/__init__.py?at=default#cl-295
Hopefully someone will correct me if I am wro
Thanks Dannon,
I set java to open the console (I assume that's what you are referring to)
but when going to galaxy it doesn't open. The console does open when i go
to java.com and verify my version. i've also just removed and reinstalled
java and rebooted machine. still no history pane :(
On Fri, Mar 14, 2014 at 11:24 AM, Peter Cock wrote:
> On Thu, Mar 13, 2014 at 6:40 PM, Sanka, Ravi wrote:
>> I do not think so. Several individual datasets have been deleted (clicked
>> the upper-right X on the history item box) but no History has been
>> permanently deleted.
>>
>> Is there any i
Grepping around the code I think this is the only way a ftype
attribute on an output affects the evaluation of test data.
if attributes.get( 'ftype', None ) == 'bam':
local_fh, temp_name = self._bam_to_sam(
local_name, temp_name )
local_name
Thanks John,
I suggest making this test framework perform this check by default
(the twill and API based frameworks) and seeing what - if anything -
breaks as a result on the Test Tool Shed.
Note that one area of fuzziness is subclasses, e.g. if the tool output
was labelled "fastqsanger", but the
The directory can be obtained using $galaxyData.extra_files_path (be
sure to check it exists before zipping it up).
I would discourage re-using Galaxy components directly from inside of
a tool or tool wrapper - but if you want to reference that code it is
actually inside of the datatypes module -
Hi Yec'han,
Sorry for the delayed response - I would guess that something is
different about the configuration of the SFTP server. Could you check
the server logs?
--nate
On Thu, Mar 6, 2014 at 8:13 AM, Yec'han Laizet
wrote:
> Hi Nate,
>
> I have reseted the password of a newly created user, so
Hmm... unfortunately I have no particular guess about either of these issues.
It sounds like you upgraded Galaxy and made large changes to your
configuration at the same time. Can you try just one process and no
load balancer so you can determine if the issue is with the Apache
configuration or th
I believe this problem was fixed by Nate after the latest dist release
and pushed to the stable branch of galaxy-central.
https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca59825d0eb3d32afd5686c4b1b9294
If you are eager for this bug fix, you can track the latest stable
branch of galax
On Wed, Mar 5, 2014 at 8:18 PM, Ravi Alla wrote:
> Hi Jennifer,
> Thank you for this information. I was able to troubleshoot the
> bowtie2_indices. Like Bjoern said the bowtie2 tool needed to be reinstalled
> because the tool_table does not load the correct indices.
>
> I am still trying to wrap m
Hi Peter,
I just wanted to add my $0.02 USD to say that I mostly agree with this
- I have long used binaries precompiled by the tool author on Main,
especially for cases where, as you say, the compile-time dependency
list is large and painful. The only "gotcha" here is to make sure that
binaries s
On Fri, Mar 14, 2014 at 4:41 PM, Nate Coraor wrote:
> Hi Peter,
>
> I just wanted to add my $0.02 USD to say that I mostly agree with this
> - I have long used binaries precompiled by the tool author on Main,
> especially for cases where, as you say, the compile-time dependency
> list is large and
On Fri, Mar 14, 2014 at 12:47 PM, Peter Cock wrote:
> On Fri, Mar 14, 2014 at 4:41 PM, Nate Coraor wrote:
>> Hi Peter,
>>
>> I just wanted to add my $0.02 USD to say that I mostly agree with this
>> - I have long used binaries precompiled by the tool author on Main,
>> especially for cases where,
Hi Nate
Thanks for the clarifications. Is there anything specific I should watch out
for when updating and deleting tools? The reason I ask is that Jennifer
mentioned in previous emails the need to update metadata for tools, which I am
sure I follow.
Thanks
Ravi
On Mar 14, 2014, at 9:02 AM, Nat
Our use was using the lastest Firefox release. I asked him to try FireFox
Portable and that seemed to do the trick. It was a problem with his
Firefox install.
Thanks for you help,
Liisa
From: Dannon Baker
To: Liisa Koski
Cc: Galaxy Dev
Date: 13/03/2014 06:39 PM
Subject:
Hmm... I can import older workflows on usegalaxy.org so I don't think
it is a general problem with all workflows as a part of the latest
release. That said I don't know what the problem is - if it is a bug
with a new release or a problem with one of your tools etc
If I had to guess I would say
This is strange.
After restarting galaxy to include the debug tool, all galaxy_slots
values are correctly assigned (tested for BWA and GATK as rerun of
original posted jobs)
If you still need the output, let me know.
Best,
Geert
On 03/14/2014 03:25 PM, John Chilton wrote:
I am not sur
Good to hear you've worked around it! For future reference, in Firefox you
can open the javascript console by clicking the "Firefox" (menu at the
top)->"Web Developer"->"Web Console". That, or Control/Command+Shift+K.
On Fri, Mar 14, 2014 at 1:49 PM, Liisa Koski wrote:
> Our use was using the
Dear galaxy-dev,
After exchanges with Eric we have decided to create:
-a common puppet module for galaxy hosted on the puppet forge:
https://forge.puppetlabs.com/urgi/galaxy
-a common repository hosted on a public server:
We want to have the opinion of the galaxy-team and galaxy-dev community
fo
I love this effort! I would recommend posting these on github instead
of bitbucket - I think it has become kind of a puppet best practice to
host collaborative repositories such as these there.
For what it is worth - I have a set of puppet modules for hosting
Galaxy that have a dependency on the p
On Fri, Mar 14, 2014 at 9:01 AM, John Chilton wrote:
> I believe this problem was fixed by Nate after the latest dist release
> and pushed to the stable branch of galaxy-central.
>
> https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca59825d0eb3d32afd5686c4b1b9294
>
> If you are eager f
Hello Tool Developers,
Haven't known when to send this out, but I figure since you haven't
received any e-mail from me today it might be a good time.
tl;dr - Tool functional tests experienced a significant overhaul over
the last release and will continue to change over the next couple
releases, b
What are the best practices for updating galaxy? Also is there a quick command
I can run to see what version of galaxy I am running?
On Mar 14, 2014, at 12:23 PM, Brian Claywell wrote:
> On Fri, Mar 14, 2014 at 9:01 AM, John Chilton wrote:
>> I believe this problem was fixed by Nate after the l
On Fri, Mar 14, 2014 at 10:24 AM, Peter Cock wrote:
> Thanks John,
>
> I suggest making this test framework perform this check by default
> (the twill and API based frameworks) and seeing what - if anything -
> breaks as a result on the Test Tool Shed.
Hey Peter,
I hope it is okay, but I do not
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