Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-17 Thread Joachim Jacob | VIB | 
Allright. I just pulled in all changesets from stable to my cloud 
Galaxy, restarted, and everything works, at first glance.


Thanks for your support!

J

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 05:21 PM, Dannon Baker wrote:
Sorry, what I was saying was that you *can* pull these changes without 
leaving stable using 'hg pull -b stable 
http://bitbucket.org/galaxy/galaxy-central'.  (Actually, if you're 
already on stable the -b is unnecessary -- you'll get the extra 
changesets but they won't be activated when you update)



On Thu, May 16, 2013 at 11:08 AM, Joachim Jacob | VIB | 
mailto:joachim.ja...@vib.be>> wrote:


OK. So I believe I can wait for the next stable release then. I
assume a do not want to go the default branch.

thanks,
Joachim


Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 05:01 PM, Dannon Baker wrote:

Your instance isn't quite up-to-date enough for the fix --
it's around 9549:47ddf167c9f1 -central / 9452:94caae7433a7
grafted in -stable.


On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB |
mailto:joachim.ja...@vib.be>
>>
wrote:

Running the Cloud Galaxy:

galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg
summary
parent: 9232:75f09617abaa release_2013.04.01
 Merge next-stable to stable for release.
branch: stable
commit: 2 modified, 9 unknown (new branch head)
update: 30 new changesets (update)
galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg branch
stable

Our production Galaxy:

[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9292:2cc8d10988e0 security_2013.04.08
 controllers/history: use get_history in switch_to_history
branch: stable
commit: 4 modified, 267 unknown (new branch head)
update: 11 new changesets (update)
[galaxy@galaxy galaxy-dist]$ hg branch
stable


Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 

Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 04:35 PM, Dannon Baker wrote:

I should have read the rest of my email before
replying -- so
you did update Galaxy for your cloud instance.  What exact
revision/branch are you running now?  There was a
brief period
when select2 was enabled for the workflow page and it
broke
things.  This should be fixed in -stable (and, of
course, tip
of -central).




On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB |
mailto:joachim.ja...@vib.be>
>

Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Dannon Baker 
Sorry, what I was saying was that you *can* pull these changes without
leaving stable using 'hg pull -b stable
http://bitbucket.org/galaxy/galaxy-central'.  (Actually, if you're already
on stable the -b is unnecessary -- you'll get the extra changesets but they
won't be activated when you update)


On Thu, May 16, 2013 at 11:08 AM, Joachim Jacob | VIB | <
joachim.ja...@vib.be> wrote:

> OK. So I believe I can wait for the next stable release then. I assume a
> do not want to go the default branch.
>
> thanks,
> Joachim
>
>
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 05/16/2013 05:01 PM, Dannon Baker wrote:
>
>> Your instance isn't quite up-to-date enough for the fix -- it's around
>> 9549:47ddf167c9f1 -central / 9452:94caae7433a7 grafted in -stable.
>>
>>
>> On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB | <
>> joachim.ja...@vib.be > wrote:
>>
>> Running the Cloud Galaxy:
>>
>> galaxy@ip-10-39-130-141:/mnt/**galaxyTools/galaxy-central$ hg summary
>> parent: 9232:75f09617abaa release_2013.04.01
>>  Merge next-stable to stable for release.
>> branch: stable
>> commit: 2 modified, 9 unknown (new branch head)
>> update: 30 new changesets (update)
>> galaxy@ip-10-39-130-141:/mnt/**galaxyTools/galaxy-central$ hg branch
>> stable
>>
>> Our production Galaxy:
>>
>> [galaxy@galaxy galaxy-dist]$ hg summary
>> parent: 9292:2cc8d10988e0 security_2013.04.08
>>  controllers/history: use get_history in switch_to_history
>> branch: stable
>> commit: 4 modified, 267 unknown (new branch head)
>> update: 11 new changesets (update)
>> [galaxy@galaxy galaxy-dist]$ hg branch
>> stable
>>
>>
>> Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> On 05/16/2013 04:35 PM, Dannon Baker wrote:
>>
>> I should have read the rest of my email before replying -- so
>> you did update Galaxy for your cloud instance.  What exact
>> revision/branch are you running now?  There was a brief period
>> when select2 was enabled for the workflow page and it broke
>> things.  This should be fixed in -stable (and, of course, tip
>> of -central).
>>
>>
>>
>>
>> On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB |
>> mailto:joachim.ja...@vib.be>
>> >**>
>>
>> wrote:
>>
>> Hi all,
>>
>>
>> I just found out that I cannot select multiple inputs in
>> workflows
>> anymore in our local Galaxy. This option used to work on these
>> workflows in the past. I only get now a dropdown box,
>> without the
>> little icon at the top of the input list to select
>> multiple inputs.
>>
>> I am a little puzzled of what's wrong. Any light in the dark?
>>
>> I have repeated these steps in a freshly started cloud galaxy
>> instance, updated to the latest release, and imported that
>> workflow. In that instance, I can select multiple files:
>> but it is
>> not anymore with the multiple selection, but in a
>> 'dropdown-checkbox-list' (hope this is clear). The problem
>> is here
>> that only one input gets processed, even the input list
>> contains
>> multiple items. Every item that is checked gets into the
>> inputbox.
>> A second issue is that this entry (already in the input
>> list) is
>> not removed from the checkbox-list: so you can select multiple
>> times the same input. (although this might be wanted in
>> some cases?)
>>
>>
>>
>> Thanks,
>> Joachim
>>
>> -- Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>> 
>>
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> 
>> http://galaxyproject.org/**search/mailinglists/
>>
>>
>>
>>
>>
>
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Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Joachim Jacob | VIB | 
OK. So I believe I can wait for the next stable release then. I assume a 
do not want to go the default branch.


thanks,
Joachim

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 05:01 PM, Dannon Baker wrote:
Your instance isn't quite up-to-date enough for the fix -- it's around 
9549:47ddf167c9f1 -central / 9452:94caae7433a7 grafted in -stable.



On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB | 
mailto:joachim.ja...@vib.be>> wrote:


Running the Cloud Galaxy:

galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg summary
parent: 9232:75f09617abaa release_2013.04.01
 Merge next-stable to stable for release.
branch: stable
commit: 2 modified, 9 unknown (new branch head)
update: 30 new changesets (update)
galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg branch
stable

Our production Galaxy:

[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9292:2cc8d10988e0 security_2013.04.08
 controllers/history: use get_history in switch_to_history
branch: stable
commit: 4 modified, 267 unknown (new branch head)
update: 11 new changesets (update)
[galaxy@galaxy galaxy-dist]$ hg branch
stable


Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 04:35 PM, Dannon Baker wrote:

I should have read the rest of my email before replying -- so
you did update Galaxy for your cloud instance.  What exact
revision/branch are you running now?  There was a brief period
when select2 was enabled for the workflow page and it broke
things.  This should be fixed in -stable (and, of course, tip
of -central).




On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB |
mailto:joachim.ja...@vib.be>
>>
wrote:

Hi all,


I just found out that I cannot select multiple inputs in
workflows
anymore in our local Galaxy. This option used to work on these
workflows in the past. I only get now a dropdown box,
without the
little icon at the top of the input list to select
multiple inputs.

I am a little puzzled of what's wrong. Any light in the dark?

I have repeated these steps in a freshly started cloud galaxy
instance, updated to the latest release, and imported that
workflow. In that instance, I can select multiple files:
but it is
not anymore with the multiple selection, but in a
'dropdown-checkbox-list' (hope this is clear). The problem
is here
that only one input gets processed, even the input list
contains
multiple items. Every item that is checked gets into the
inputbox.
A second issue is that this entry (already in the input
list) is
not removed from the checkbox-list: so you can select multiple
times the same input. (although this might be wanted in
some cases?)



Thanks,
Joachim

-- Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 


Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Dannon Baker 
Your instance isn't quite up-to-date enough for the fix -- it's around
9549:47ddf167c9f1 -central / 9452:94caae7433a7 grafted in -stable.


On Thu, May 16, 2013 at 10:56 AM, Joachim Jacob | VIB | <
joachim.ja...@vib.be> wrote:

> Running the Cloud Galaxy:
>
> galaxy@ip-10-39-130-141:/mnt/**galaxyTools/galaxy-central$ hg summary
> parent: 9232:75f09617abaa release_2013.04.01
>  Merge next-stable to stable for release.
> branch: stable
> commit: 2 modified, 9 unknown (new branch head)
> update: 30 new changesets (update)
> galaxy@ip-10-39-130-141:/mnt/**galaxyTools/galaxy-central$ hg branch
> stable
>
> Our production Galaxy:
>
> [galaxy@galaxy galaxy-dist]$ hg summary
> parent: 9292:2cc8d10988e0 security_2013.04.08
>  controllers/history: use get_history in switch_to_history
> branch: stable
> commit: 4 modified, 267 unknown (new branch head)
> update: 11 new changesets (update)
> [galaxy@galaxy galaxy-dist]$ hg branch
> stable
>
>
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 05/16/2013 04:35 PM, Dannon Baker wrote:
>
>> I should have read the rest of my email before replying -- so you did
>> update Galaxy for your cloud instance.  What exact revision/branch are you
>> running now?  There was a brief period when select2 was enabled for the
>> workflow page and it broke things.  This should be fixed in -stable (and,
>> of course, tip of -central).
>>
>>
>>
>>
>> On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB | <
>> joachim.ja...@vib.be > wrote:
>>
>> Hi all,
>>
>>
>> I just found out that I cannot select multiple inputs in workflows
>> anymore in our local Galaxy. This option used to work on these
>> workflows in the past. I only get now a dropdown box, without the
>> little icon at the top of the input list to select multiple inputs.
>>
>> I am a little puzzled of what's wrong. Any light in the dark?
>>
>> I have repeated these steps in a freshly started cloud galaxy
>> instance, updated to the latest release, and imported that
>> workflow. In that instance, I can select multiple files: but it is
>> not anymore with the multiple selection, but in a
>> 'dropdown-checkbox-list' (hope this is clear). The problem is here
>> that only one input gets processed, even the input list contains
>> multiple items. Every item that is checked gets into the inputbox.
>> A second issue is that this entry (already in the input list) is
>> not removed from the checkbox-list: so you can select multiple
>> times the same input. (although this might be wanted in some cases?)
>>
>>
>>
>> Thanks,
>> Joachim
>>
>> -- Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>>
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> __**_
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> 
>> http://galaxyproject.org/**search/mailinglists/
>>
>>
>>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Joachim Jacob | VIB | 

Running the Cloud Galaxy:

galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg summary
parent: 9232:75f09617abaa release_2013.04.01
 Merge next-stable to stable for release.
branch: stable
commit: 2 modified, 9 unknown (new branch head)
update: 30 new changesets (update)
galaxy@ip-10-39-130-141:/mnt/galaxyTools/galaxy-central$ hg branch
stable

Our production Galaxy:

[galaxy@galaxy galaxy-dist]$ hg summary
parent: 9292:2cc8d10988e0 security_2013.04.08
 controllers/history: use get_history in switch_to_history
branch: stable
commit: 4 modified, 267 unknown (new branch head)
update: 11 new changesets (update)
[galaxy@galaxy galaxy-dist]$ hg branch
stable

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/16/2013 04:35 PM, Dannon Baker wrote:
I should have read the rest of my email before replying -- so you did 
update Galaxy for your cloud instance.  What exact revision/branch are 
you running now?  There was a brief period when select2 was enabled 
for the workflow page and it broke things.  This should be fixed in 
-stable (and, of course, tip of -central).





On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB | 
mailto:joachim.ja...@vib.be>> wrote:


Hi all,


I just found out that I cannot select multiple inputs in workflows
anymore in our local Galaxy. This option used to work on these
workflows in the past. I only get now a dropdown box, without the
little icon at the top of the input list to select multiple inputs.

I am a little puzzled of what's wrong. Any light in the dark?

I have repeated these steps in a freshly started cloud galaxy
instance, updated to the latest release, and imported that
workflow. In that instance, I can select multiple files: but it is
not anymore with the multiple selection, but in a
'dropdown-checkbox-list' (hope this is clear). The problem is here
that only one input gets processed, even the input list contains
multiple items. Every item that is checked gets into the inputbox.
A second issue is that this entry (already in the input list) is
not removed from the checkbox-list: so you can select multiple
times the same input. (although this might be wanted in some cases?)



Thanks,
Joachim

-- 
Joachim Jacob


Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Dannon Baker 
I should have read the rest of my email before replying -- so you did
update Galaxy for your cloud instance.  What exact revision/branch are you
running now?  There was a brief period when select2 was enabled for the
workflow page and it broke things.  This should be fixed in -stable (and,
of course, tip of -central).




On Thu, May 16, 2013 at 10:12 AM, Joachim Jacob | VIB | <
joachim.ja...@vib.be> wrote:

> Hi all,
>
>
> I just found out that I cannot select multiple inputs in workflows anymore
> in our local Galaxy. This option used to work on these workflows in the
> past. I only get now a dropdown box, without the little icon at the top of
> the input list to select multiple inputs.
>
> I am a little puzzled of what's wrong. Any light in the dark?
>
> I have repeated these steps in a freshly started cloud galaxy instance,
> updated to the latest release, and imported that workflow. In that
> instance, I can select multiple files: but it is not anymore with the
> multiple selection, but in a 'dropdown-checkbox-list' (hope this is clear).
> The problem is here that only one input gets processed, even the input list
> contains multiple items. Every item that is checked gets into the inputbox.
> A second issue is that this entry (already in the input list) is not
> removed from the checkbox-list: so you can select multiple times the same
> input. (although this might be wanted in some cases?)
>
>
>
> Thanks,
> Joachim
>
> --
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  
> http://galaxyproject.org/**search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] selecting multiple inputs for workflows not possible

2013-05-16 Thread Dannon Baker 
This is probably related to the galaxy version currently available by
default in the cloud -- it's significantly out of date.  We froze updates
to the base volume pending a new Cloudman release (that shouldn't be too
much longer in development).

You should be able to update the galaxy installation for your cluster to
the latest -stable and try again.

-Dannon


On Thu, May 16, 2013 at 9:59 AM, Joachim Jacob | VIB |  wrote:

> Hi all,
>
>
> I just found out that I cannot select multiple inputs in workflows. This
> option used to work on these workflows in the past.
>
> I am a little puzzled of what's wrong. Any light in the dark? Note: I have
> started a cloud galaxy instance and imported that workflow, but no option
> to select multiple inputs.
>
>
> Thanks,
> Joachim
>
> --
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> __**_
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  
> http://galaxyproject.org/**search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] selecting multiple inputs for workflows not possible anymore

2013-05-16 Thread Joachim Jacob | VIB | 

Hi all,


I just found out that I cannot select multiple inputs in workflows 
anymore in our local Galaxy. This option used to work on these workflows 
in the past. I only get now a dropdown box, without the little icon at 
the top of the input list to select multiple inputs.


I am a little puzzled of what's wrong. Any light in the dark?

I have repeated these steps in a freshly started cloud galaxy instance, 
updated to the latest release, and imported that workflow. In that 
instance, I can select multiple files: but it is not anymore with the 
multiple selection, but in a 'dropdown-checkbox-list' (hope this is 
clear). The problem is here that only one input gets processed, even the 
input list contains multiple items. Every item that is checked gets into 
the inputbox. A second issue is that this entry (already in the input 
list) is not removed from the checkbox-list: so you can select multiple 
times the same input. (although this might be wanted in some cases?)




Thanks,
Joachim

--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

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[galaxy-dev] selecting multiple inputs for workflows not possible

2013-05-16 Thread Joachim Jacob | VIB | 

Hi all,


I just found out that I cannot select multiple inputs in workflows. This 
option used to work on these workflows in the past.


I am a little puzzled of what's wrong. Any light in the dark? Note: I 
have started a cloud galaxy instance and imported that workflow, but no 
option to select multiple inputs.



Thanks,
Joachim

--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/