Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Björn Grüning]

Am 15.10.2015 um 09:46 schrieb Sebastian Schaaf:
> Hi Björn,
> 
> The discussion looks good, although (or right because?) it gained a
> somewhat more generic scope, where QIIME is one of several construction
> sites in the metagenomics field. Do I get it right that the date for the
> hackathon is tba? Will there be a notification? I think we would like to
> join :).

Yes, we are trying find a schedule :)
Subscribe to the github issue and you will know. We will also announce
it via twitter and this ML.

> Anyhow we discussed yesterday in the office and came up the following:
> 
> 1. Ashok collected all dependencies (names/versions of tools/libraries),
> he also formalized them in recipes. The community has to check whether
> it fits the needs/expectations, as we are relatively new to tool sheds
> and started to load a private one recently with tools. But the plain
> list should already save some work. As we run SLES as OS (which is close
> to blank in terms of up to date software...) the dependency list should
> go quite far.


Awesome. Please see also this one here:
https://github.com/galaxyproject/tools-iuc/pull/297

It takes care of all python libs. Testing and enhancements are welcome!
Depending on how far we will get with wrapping tools we also need the
other dependencies.


> 2. The codes which were written by him for an internship will anyhow get
> some improvements: currently the "qiime_connector" is simply a kind of
> archive extractor which makes an arbitrary file from a QIIME tool output
> archive available in the Galaxy history, so that there is neither a dead
> end nor the need for a "download/upload" step. For user who know QIIME
> from the command line (and therefore know how the modules work) this may
> be a suitable solution, but not for beginners who start with
> metagenomics. Somehow it does not feel "galaxy'sh"...

Also a nice ideas. I guess we discuss this in more detail during the
hackathon and trying to get some proper filetypes into Galaxy for this.

> So far, looking forward to joining forces :).

!!!
Greetings to Munich!
Bjoern

> Cheers,
> Sebastian
> 
> 
> Björn Grüning schrieb:
>> Hi Sebastian,
>>
>> I think we try to work on this during our upcoming hackathon.
>>
>> https://github.com/galaxyproject/tools-iuc/issues/299
>>
>> It would be nice to join and contribute your work to it.
>>
>> Thanks,
>> Bjoern
>>
>> Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:
>>> Hey there,
>>>
>>> Any news on this?
>>>
>>> My colleague Aarif made me aware of the discussion, because one of our
>>> students, Ashok, worked on this months ago. QIIME was requested by a
>>> project which never started and therefore the developed codes did not
>>> gain priority. Basically we faced the same issues, and at least the
>>> 'dead end' problem with the resulting tgz archives was solved. We are
>>> currently assembling the codes into a toolshed entry, but I need to ask
>>> Ashok tomorrow about the current progress.
>>>
>>> Is there still interest on it or is everything already on the move..?
>>>
>>> Cheers,
>>>
>>> Sebastian
>>>
>>>
>>> Björn Grüning schrieb:
>>>> Hi Yvan,
>>>>
>>>>> Hi Lance, Björn, Dan
>>>>>
>>>>> We are several scientists working on metagenomics in France and at a
>>>>> previous GUGGO  (western France User Group) meeting, we mention the
>>>>> fact to "benchmark" our Galaxy pipelines. One is using new Qiime
>>>>> tools integration, one Mothur and the last one, the recently
>>>>> developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline
>>>>> using Swarm. We already have had some exchanges with Björn concerning
>>>>> metagenomics flavours on Docker, and I think it will be particularly
>>>>> interesting to exchange one with each other. The Qiime integration
>>>>> was started in march by colleagues from Brest Ifremer centre. I was
>>>>> just trying to install and test FROGS from Toulouse and Jouy-en-Josas
>>>>> INRA labs. If they are not on the list, I can contact them.
>>>> Please do so. This is great to know. Please also consider to join our
>>>> hackathon:
>>>>
>>>> https://github.com/galaxyproject/tools-iuc/issues/299
>>>>
>>>> We are always open for new ideas. Would be great to get a nice suite
>>>> and
>>>> a few workflows for metagenomic in the near future! :)
>>>

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Sebastian Schaaf]

Hi Björn,

The discussion looks good, although (or right because?) it gained a 
somewhat more generic scope, where QIIME is one of several construction 
sites in the metagenomics field. Do I get it right that the date for the 
hackathon is tba? Will there be a notification? I think we would like to 
join :).


Anyhow we discussed yesterday in the office and came up the following:

1. Ashok collected all dependencies (names/versions of tools/libraries), 
he also formalized them in recipes. The community has to check whether 
it fits the needs/expectations, as we are relatively new to tool sheds 
and started to load a private one recently with tools. But the plain 
list should already save some work. As we run SLES as OS (which is close 
to blank in terms of up to date software...) the dependency list should 
go quite far.


2. The codes which were written by him for an internship will anyhow get 
some improvements: currently the "qiime_connector" is simply a kind of 
archive extractor which makes an arbitrary file from a QIIME tool output 
archive available in the Galaxy history, so that there is neither a dead 
end nor the need for a "download/upload" step. For user who know QIIME 
from the command line (and therefore know how the modules work) this may 
be a suitable solution, but not for beginners who start with 
metagenomics. Somehow it does not feel "galaxy'sh"...


So far, looking forward to joining forces :).

Cheers,
Sebastian


Björn Grüning schrieb:

Hi Sebastian,

I think we try to work on this during our upcoming hackathon.

https://github.com/galaxyproject/tools-iuc/issues/299

It would be nice to join and contribute your work to it.

Thanks,
Bjoern

Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:

Hey there,

Any news on this?

My colleague Aarif made me aware of the discussion, because one of our
students, Ashok, worked on this months ago. QIIME was requested by a
project which never started and therefore the developed codes did not
gain priority. Basically we faced the same issues, and at least the
'dead end' problem with the resulting tgz archives was solved. We are
currently assembling the codes into a toolshed entry, but I need to ask
Ashok tomorrow about the current progress.

Is there still interest on it or is everything already on the move..?

Cheers,

Sebastian


Björn Grüning schrieb:

Hi Yvan,


Hi Lance, Björn, Dan

We are several scientists working on metagenomics in France and at a
previous GUGGO  (western France User Group) meeting, we mention the
fact to "benchmark" our Galaxy pipelines. One is using new Qiime
tools integration, one Mothur and the last one, the recently
developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline
using Swarm. We already have had some exchanges with Björn concerning
metagenomics flavours on Docker, and I think it will be particularly
interesting to exchange one with each other. The Qiime integration
was started in march by colleagues from Brest Ifremer centre. I was
just trying to install and test FROGS from Toulouse and Jouy-en-Josas
INRA labs. If they are not on the list, I can contact them.

Please do so. This is great to know. Please also consider to join our
hackathon:

https://github.com/galaxyproject/tools-iuc/issues/299

We are always open for new ideas. Would be great to get a nice suite and
a few workflows for metagenomic in the near future! :)

Thanks,
Bjoern


All the best,

Yvan

- Mail original -

De: "Björn Grüning"  À: "Lance Parsons"
, "Daniel Blankenberg"  Cc:
"Galaxy Dev List"  Envoyé:
Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME
tools for Galaxy (WIP,call for collaborators)

Hi Lance,

I will help if I can. I also think we should begin too write 2-3
nice tools in the beginning to test the handshake between them and
lay the ground work. This will also help to get familiar with the
tool.

I still hope some one else from the community shows interest! :)

Thanks, Bjoern

Am 06.10.2015 um 20:33 schrieb Lance Parsons:

I agree that it would be very nice to get the data flowing
between each of the tools and to be able to mix/match with other
tools. That is an area of Galaxy tool-dev that I'm less familiar
with, so any help would be greatly appreciated.

As for the manual massaging, I agree, however, at this point I'm
really hoping that the changes between Qiime versions are
manageable, esp. once we have the data types and basic framework
of the tools down.

Along that front, I would very much like to get something usable
(at least for some specific workflows) done sooner rather than
later, then be able to iterate, adding new tools, datatypes, etc.
as we move forward. Does that sound reasonable? I love the idea
of a Metagenomics toolfest
(https://github.com/galaxyproject/tools-iuc/issues/299). One
thing I would like to do soon then, would be to define some
functionality for the first roun

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Björn Grüning]

Hi Sebastian,

I think we try to work on this during our upcoming hackathon.

https://github.com/galaxyproject/tools-iuc/issues/299

It would be nice to join and contribute your work to it.

Thanks,
Bjoern

Am 13.10.2015 um 15:03 schrieb Sebastian Schaaf:
> Hey there,
> 
> Any news on this?
> 
> My colleague Aarif made me aware of the discussion, because one of our
> students, Ashok, worked on this months ago. QIIME was requested by a
> project which never started and therefore the developed codes did not
> gain priority. Basically we faced the same issues, and at least the
> 'dead end' problem with the resulting tgz archives was solved. We are
> currently assembling the codes into a toolshed entry, but I need to ask
> Ashok tomorrow about the current progress.
> 
> Is there still interest on it or is everything already on the move..?
> 
> Cheers,
> 
> Sebastian
> 
> 
> Björn Grüning schrieb:
>> Hi Yvan,
>>
>>> Hi Lance, Björn, Dan
>>>
>>> We are several scientists working on metagenomics in France and at a
>>> previous GUGGO  (western France User Group) meeting, we mention the
>>> fact to "benchmark" our Galaxy pipelines. One is using new Qiime
>>> tools integration, one Mothur and the last one, the recently
>>> developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline
>>> using Swarm. We already have had some exchanges with Björn concerning
>>> metagenomics flavours on Docker, and I think it will be particularly
>>> interesting to exchange one with each other. The Qiime integration
>>> was started in march by colleagues from Brest Ifremer centre. I was
>>> just trying to install and test FROGS from Toulouse and Jouy-en-Josas
>>> INRA labs. If they are not on the list, I can contact them.
>> Please do so. This is great to know. Please also consider to join our
>> hackathon:
>>
>> https://github.com/galaxyproject/tools-iuc/issues/299
>>
>> We are always open for new ideas. Would be great to get a nice suite and
>> a few workflows for metagenomic in the near future! :)
>>
>> Thanks,
>> Bjoern
>>
>>> All the best,
>>>
>>> Yvan
>>>
>>> - Mail original -
>>>> De: "Björn Grüning"  À: "Lance Parsons"
>>>> , "Daniel Blankenberg"  Cc:
>>>> "Galaxy Dev List"  Envoyé:
>>>> Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME
>>>> tools for Galaxy (WIP,call for collaborators)
>>>>
>>>> Hi Lance,
>>>>
>>>> I will help if I can. I also think we should begin too write 2-3
>>>> nice tools in the beginning to test the handshake between them and
>>>> lay the ground work. This will also help to get familiar with the
>>>> tool.
>>>>
>>>> I still hope some one else from the community shows interest! :)
>>>>
>>>> Thanks, Bjoern
>>>>
>>>> Am 06.10.2015 um 20:33 schrieb Lance Parsons:
>>>>> I agree that it would be very nice to get the data flowing
>>>>> between each of the tools and to be able to mix/match with other
>>>>> tools. That is an area of Galaxy tool-dev that I'm less familiar
>>>>> with, so any help would be greatly appreciated.
>>>>>
>>>>> As for the manual massaging, I agree, however, at this point I'm
>>>>> really hoping that the changes between Qiime versions are
>>>>> manageable, esp. once we have the data types and basic framework
>>>>> of the tools down.
>>>>>
>>>>> Along that front, I would very much like to get something usable
>>>>> (at least for some specific workflows) done sooner rather than
>>>>> later, then be able to iterate, adding new tools, datatypes, etc.
>>>>> as we move forward. Does that sound reasonable? I love the idea
>>>>> of a Metagenomics toolfest
>>>>> (https://github.com/galaxyproject/tools-iuc/issues/299). One
>>>>> thing I would like to do soon then, would be to define some
>>>>> functionality for the first round. What would be very helpful
>>>>> would be if you, Bjoern, etc. could help make sure the first
>>>>> round lays the proper groundwork so I/we don't have to redo
>>>>> things for later iterations, but we can build on a solid
>>>>> foundation.
>>>>>
>>>>> Thanks so much for the input, help, etc. It is very muc

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Sebastian Schaaf]

Hey there,

Any news on this?

My colleague Aarif made me aware of the discussion, because one of our 
students, Ashok, worked on this months ago. QIIME was requested by a 
project which never started and therefore the developed codes did not 
gain priority. Basically we faced the same issues, and at least the 
'dead end' problem with the resulting tgz archives was solved. We are 
currently assembling the codes into a toolshed entry, but I need to ask 
Ashok tomorrow about the current progress.


Is there still interest on it or is everything already on the move..?

Cheers,

Sebastian


Björn Grüning schrieb:

Hi Yvan,


Hi Lance, Björn, Dan

We are several scientists working on metagenomics in France and at a
previous GUGGO  (western France User Group) meeting, we mention the
fact to "benchmark" our Galaxy pipelines. One is using new Qiime
tools integration, one Mothur and the last one, the recently
developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline
using Swarm. We already have had some exchanges with Björn concerning
metagenomics flavours on Docker, and I think it will be particularly
interesting to exchange one with each other. The Qiime integration
was started in march by colleagues from Brest Ifremer centre. I was
just trying to install and test FROGS from Toulouse and Jouy-en-Josas
INRA labs. If they are not on the list, I can contact them.

Please do so. This is great to know. Please also consider to join our
hackathon:

https://github.com/galaxyproject/tools-iuc/issues/299

We are always open for new ideas. Would be great to get a nice suite and
a few workflows for metagenomic in the near future! :)

Thanks,
Bjoern


All the best,

Yvan

- Mail original -

De: "Björn Grüning"  À: "Lance Parsons"
, "Daniel Blankenberg"  Cc:
"Galaxy Dev List"  Envoyé:
Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME
tools for Galaxy (WIP,  call for collaborators)

Hi Lance,

I will help if I can. I also think we should begin too write 2-3
nice tools in the beginning to test the handshake between them and
lay the ground work. This will also help to get familiar with the
tool.

I still hope some one else from the community shows interest! :)

Thanks, Bjoern

Am 06.10.2015 um 20:33 schrieb Lance Parsons:

I agree that it would be very nice to get the data flowing
between each of the tools and to be able to mix/match with other
tools. That is an area of Galaxy tool-dev that I'm less familiar
with, so any help would be greatly appreciated.

As for the manual massaging, I agree, however, at this point I'm
really hoping that the changes between Qiime versions are
manageable, esp. once we have the data types and basic framework
of the tools down.

Along that front, I would very much like to get something usable
(at least for some specific workflows) done sooner rather than
later, then be able to iterate, adding new tools, datatypes, etc.
as we move forward. Does that sound reasonable? I love the idea
of a Metagenomics toolfest
(https://github.com/galaxyproject/tools-iuc/issues/299). One
thing I would like to do soon then, would be to define some
functionality for the first round. What would be very helpful
would be if you, Bjoern, etc. could help make sure the first
round lays the proper groundwork so I/we don't have to redo
things for later iterations, but we can build on a solid
foundation.

Thanks so much for the input, help, etc. It is very much
appreciated.

- Lance


Daniel Blankenberg <mailto:d...@bx.psu.edu> October 6, 2015 at
10:21 AM Hi Lance,

I looked at this a bit ago and had similar concerns,
particularly with the outputs and inputs not being
well-defined. In addition to the output tar ball —> local,
extract —> upload not being great, as you mention, the input
datatypes, etc, could use some work — in the very least, we
should definitely create a nice biom datatype and have some
converters available (import and export).

Definitely worth spending some extra time to make sure that we
have the data flowing well between each of the different
parts/tools, and even better to make sure that its done in a
way that allows mixing and matching with other non-qiime
tools.


One thing that we want to avoid is large amounts of manual
massaging of the automatically generated xml; fixing things up
once might not be too bad, but having to do it with each new
tool version can be “frustrating". Although perhaps having a
good starting point and only needing to manually modify for any
updates could be good enough (I’m not very familiar with the
extent of typical changes between qiime versions to make a call
on how much changes).




Dan

(resending since I received a message bounce from list)



Daniel Blankenberg <mailto:d...@bx.psu.edu> October 6, 2015 at
9:59 AM Hi Lance,

I looked at this a bit ago and had similar concerns,
particularly with the outputs and inputs not being
well-defined. I

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Björn Grüning]

Hi Yvan,

> Hi Lance, Björn, Dan
> 
> We are several scientists working on metagenomics in France and at a
> previous GUGGO  (western France User Group) meeting, we mention the
> fact to "benchmark" our Galaxy pipelines. One is using new Qiime
> tools integration, one Mothur and the last one, the recently
> developped FROGS (Find Rapidly OTU with Galaxy Solution) pipeline
> using Swarm. We already have had some exchanges with Björn concerning
> metagenomics flavours on Docker, and I think it will be particularly
> interesting to exchange one with each other. The Qiime integration
> was started in march by colleagues from Brest Ifremer centre. I was
> just trying to install and test FROGS from Toulouse and Jouy-en-Josas
> INRA labs. If they are not on the list, I can contact them.

Please do so. This is great to know. Please also consider to join our
hackathon:

https://github.com/galaxyproject/tools-iuc/issues/299

We are always open for new ideas. Would be great to get a nice suite and
a few workflows for metagenomic in the near future! :)

Thanks,
Bjoern

> All the best,
> 
> Yvan
> 
> - Mail original -
>> De: "Björn Grüning"  À: "Lance Parsons"
>> , "Daniel Blankenberg"  Cc:
>> "Galaxy Dev List"  Envoyé:
>> Mercredi 7 Octobre 2015 14:25:38 Objet: Re: [galaxy-dev] QIIME
>> tools for Galaxy (WIP,   call for collaborators)
>> 
>> Hi Lance,
>> 
>> I will help if I can. I also think we should begin too write 2-3
>> nice tools in the beginning to test the handshake between them and
>> lay the ground work. This will also help to get familiar with the
>> tool.
>> 
>> I still hope some one else from the community shows interest! :)
>> 
>> Thanks, Bjoern
>> 
>> Am 06.10.2015 um 20:33 schrieb Lance Parsons:
>>> I agree that it would be very nice to get the data flowing
>>> between each of the tools and to be able to mix/match with other
>>> tools. That is an area of Galaxy tool-dev that I'm less familiar
>>> with, so any help would be greatly appreciated.
>>> 
>>> As for the manual massaging, I agree, however, at this point I'm
>>> really hoping that the changes between Qiime versions are
>>> manageable, esp. once we have the data types and basic framework
>>> of the tools down.
>>> 
>>> Along that front, I would very much like to get something usable
>>> (at least for some specific workflows) done sooner rather than
>>> later, then be able to iterate, adding new tools, datatypes, etc.
>>> as we move forward. Does that sound reasonable? I love the idea
>>> of a Metagenomics toolfest
>>> (https://github.com/galaxyproject/tools-iuc/issues/299). One 
>>> thing I would like to do soon then, would be to define some 
>>> functionality for the first round. What would be very helpful
>>> would be if you, Bjoern, etc. could help make sure the first
>>> round lays the proper groundwork so I/we don't have to redo
>>> things for later iterations, but we can build on a solid
>>> foundation.
>>> 
>>> Thanks so much for the input, help, etc. It is very much
>>> appreciated.
>>> 
>>> - Lance
>>> 
>>>> Daniel Blankenberg <mailto:d...@bx.psu.edu> October 6, 2015 at
>>>> 10:21 AM Hi Lance,
>>>> 
>>>> I looked at this a bit ago and had similar concerns,
>>>> particularly with the outputs and inputs not being
>>>> well-defined. In addition to the output tar ball —> local,
>>>> extract —> upload not being great, as you mention, the input
>>>> datatypes, etc, could use some work — in the very least, we
>>>> should definitely create a nice biom datatype and have some 
>>>> converters available (import and export).
>>>> 
>>>> Definitely worth spending some extra time to make sure that we
>>>> have the data flowing well between each of the different
>>>> parts/tools, and even better to make sure that its done in a
>>>> way that allows mixing and matching with other non-qiime
>>>> tools.
>>>> 
>>>> 
>>>> One thing that we want to avoid is large amounts of manual
>>>> massaging of the automatically generated xml; fixing things up
>>>> once might not be too bad, but having to do it with each new
>>>> tool version can be “frustrating". Although perhaps having a
>>>> good starting point and only needing to manually modify for any
>>>> updates

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Yvan Le Bras]

Hi Lance, Björn, Dan

We are several scientists working on metagenomics in France and at a previous 
GUGGO  (western France User Group) meeting, we mention the fact to "benchmark" 
our Galaxy pipelines. One is using new Qiime tools integration, one Mothur and 
the last one, the recently developped FROGS (Find Rapidly OTU with Galaxy 
Solution) pipeline using Swarm. We already have had some exchanges with Björn 
concerning metagenomics flavours on Docker, and I think it will be particularly 
interesting to exchange one with each other. The Qiime integration was started 
in march by colleagues from Brest Ifremer centre. I was just trying to install 
and test FROGS from Toulouse and Jouy-en-Josas INRA labs. If they are not on 
the list, I can contact them.

All the best,

Yvan 

- Mail original -
> De: "Björn Grüning" 
> À: "Lance Parsons" , "Daniel Blankenberg" 
> 
> Cc: "Galaxy Dev List" 
> Envoyé: Mercredi 7 Octobre 2015 14:25:38
> Objet: Re: [galaxy-dev] QIIME tools for Galaxy (WIP,  call for collaborators)
> 
> Hi Lance,
> 
> I will help if I can. I also think we should begin too write 2-3 nice
> tools in the beginning to test the handshake between them and lay the
> ground work. This will also help to get familiar with the tool.
> 
> I still hope some one else from the community shows interest! :)
> 
> Thanks,
> Bjoern
> 
> Am 06.10.2015 um 20:33 schrieb Lance Parsons:
> > I agree that it would be very nice to get the data flowing between each
> > of the tools and to be able to mix/match with other tools. That is an
> > area of Galaxy tool-dev that I'm less familiar with, so any help would
> > be greatly appreciated.
> > 
> > As for the manual massaging, I agree, however, at this point I'm really
> > hoping that the changes between Qiime versions are manageable, esp. once
> > we have the data types and basic framework of the tools down.
> > 
> > Along that front, I would very much like to get something usable (at
> > least for some specific workflows) done sooner rather than later, then
> > be able to iterate, adding new tools, datatypes, etc. as we move
> > forward. Does that sound reasonable? I love the idea of a Metagenomics
> > toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One
> > thing I would like to do soon then, would be to define some
> > functionality for the first round. What would be very helpful would be
> > if you, Bjoern, etc. could help make sure the first round lays the
> > proper groundwork so I/we don't have to redo things for later
> > iterations, but we can build on a solid foundation.
> > 
> > Thanks so much for the input, help, etc. It is very much appreciated.
> > 
> > - Lance
> > 
> >> Daniel Blankenberg <mailto:d...@bx.psu.edu>
> >> October 6, 2015 at 10:21 AM
> >> Hi Lance,
> >>
> >> I looked at this a bit ago and had similar concerns, particularly with
> >> the outputs and inputs not being well-defined. In addition to the
> >> output tar ball —> local, extract —> upload not being great, as you
> >> mention, the input datatypes, etc, could use some work — in the very
> >> least, we should definitely create a nice biom datatype and have some
> >> converters available (import and export).
> >>
> >> Definitely worth spending some extra time to make sure that we have
> >> the data flowing well between each of the different parts/tools, and
> >> even better to make sure that its done in a way that allows mixing and
> >> matching with other non-qiime tools.
> >>
> >>
> >> One thing that we want to avoid is large amounts of manual massaging
> >> of the automatically generated xml; fixing things up once might not be
> >> too bad, but having to do it with each new tool version can be
> >> “frustrating". Although perhaps having a good starting point and only
> >> needing to manually modify for any updates could be good enough (I’m
> >> not very familiar with the extent of typical changes between qiime
> >> versions to make a call on how much changes).
> >>
> >>
> >>
> >>
> >> Dan
> >>
> >> (resending since I received a message bounce from list)
> >>
> >>
> >>
> >> Daniel Blankenberg <mailto:d...@bx.psu.edu>
> >> October 6, 2015 at 9:59 AM
> >> Hi Lance,
> >>
> >> I looked at this a bit ago and had similar concerns, particularly with
> >> the outputs and inputs not being well-defined. In addition to the
> >>

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Björn Grüning]

Hi Lance,

I will help if I can. I also think we should begin too write 2-3 nice
tools in the beginning to test the handshake between them and lay the
ground work. This will also help to get familiar with the tool.

I still hope some one else from the community shows interest! :)

Thanks,
Bjoern

Am 06.10.2015 um 20:33 schrieb Lance Parsons:
> I agree that it would be very nice to get the data flowing between each
> of the tools and to be able to mix/match with other tools. That is an
> area of Galaxy tool-dev that I'm less familiar with, so any help would
> be greatly appreciated.
> 
> As for the manual massaging, I agree, however, at this point I'm really
> hoping that the changes between Qiime versions are manageable, esp. once
> we have the data types and basic framework of the tools down.
> 
> Along that front, I would very much like to get something usable (at
> least for some specific workflows) done sooner rather than later, then
> be able to iterate, adding new tools, datatypes, etc. as we move
> forward. Does that sound reasonable? I love the idea of a Metagenomics
> toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One
> thing I would like to do soon then, would be to define some
> functionality for the first round. What would be very helpful would be
> if you, Bjoern, etc. could help make sure the first round lays the
> proper groundwork so I/we don't have to redo things for later
> iterations, but we can build on a solid foundation.
> 
> Thanks so much for the input, help, etc. It is very much appreciated.
> 
> - Lance
> 
>> Daniel Blankenberg 
>> October 6, 2015 at 10:21 AM
>> Hi Lance,
>>
>> I looked at this a bit ago and had similar concerns, particularly with
>> the outputs and inputs not being well-defined. In addition to the
>> output tar ball —> local, extract —> upload not being great, as you
>> mention, the input datatypes, etc, could use some work — in the very
>> least, we should definitely create a nice biom datatype and have some
>> converters available (import and export).
>>
>> Definitely worth spending some extra time to make sure that we have
>> the data flowing well between each of the different parts/tools, and
>> even better to make sure that its done in a way that allows mixing and
>> matching with other non-qiime tools.
>>
>>
>> One thing that we want to avoid is large amounts of manual massaging
>> of the automatically generated xml; fixing things up once might not be
>> too bad, but having to do it with each new tool version can be
>> “frustrating". Although perhaps having a good starting point and only
>> needing to manually modify for any updates could be good enough (I’m
>> not very familiar with the extent of typical changes between qiime
>> versions to make a call on how much changes).
>>
>>
>>
>>
>> Dan
>>
>> (resending since I received a message bounce from list)
>>
>>
>>
>> Daniel Blankenberg 
>> October 6, 2015 at 9:59 AM
>> Hi Lance,
>>
>> I looked at this a bit ago and had similar concerns, particularly with
>> the outputs and inputs not being well-defined. In addition to the
>> output tar ball —> local, extract —> upload not being great, as you
>> mention, the input datatypes, etc, could use some work — in the very
>> least, we should definitely create a nice biom datatype and have some
>> converters available (import and export).
>>
>> Definitely worth spending some extra time to make sure that we have
>> the data flowing well between each of the different parts/tools, and
>> even better to make sure that its done in a way that allows mixing and
>> matching with other non-qiime tools.
>>
>>
>> One thing that we want to avoid is large amounts of manual massaging
>> of the automatically generated xml; fixing things up once might not be
>> too bad, but having to do it with each new tool version can be
>> “frustrating". Although perhaps having a good starting point and only
>> needing to manually modify for any updates could be good enough (I’m
>> not very familiar with the extent of typical changes between qiime
>> versions to make a call on how much changes).
>>
>>
>>
>>
>> Dan
>>
>>
>>
>> Lance Parsons 
>> October 5, 2015 at 5:26 PM
>> I was recently asked if I could provide a QIIME analysis pipeline for
>> 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
>>
>> I did a bit of looking around for existing Galaxy wrappers and found
>> an application that generates the wrappers for QIIME scripts for
>> Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well
>> written application that does a great job of wrapping the QIIME
>> scripts for Galaxy. However, there are a few things about it that
>> don't quite fit my needs.
>>
>> 1. The tools output tgz files of all of the output files. This means
>> that to execute a pipeline, the user would have to download the tgz
>> files, untar, and then upload whichever file(s) are needed for the
>

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Lance Parsons]

I agree that it would be very nice to get the data flowing between each 
of the tools and to be able to mix/match with other tools. That is an 
area of Galaxy tool-dev that I'm less familiar with, so any help would 
be greatly appreciated.


As for the manual massaging, I agree, however, at this point I'm really 
hoping that the changes between Qiime versions are manageable, esp. once 
we have the data types and basic framework of the tools down.


Along that front, I would very much like to get something usable (at 
least for some specific workflows) done sooner rather than later, then 
be able to iterate, adding new tools, datatypes, etc. as we move 
forward. Does that sound reasonable? I love the idea of a Metagenomics 
toolfest (https://github.com/galaxyproject/tools-iuc/issues/299). One 
thing I would like to do soon then, would be to define some 
functionality for the first round. What would be very helpful would be 
if you, Bjoern, etc. could help make sure the first round lays the 
proper groundwork so I/we don't have to redo things for later 
iterations, but we can build on a solid foundation.


Thanks so much for the input, help, etc. It is very much appreciated.

- Lance


Daniel Blankenberg 
October 6, 2015 at 10:21 AM
Hi Lance,

I looked at this a bit ago and had similar concerns, particularly with 
the outputs and inputs not being well-defined. In addition to the 
output tar ball —> local, extract —> upload not being great, as you 
mention, the input datatypes, etc, could use some work — in the very 
least, we should definitely create a nice biom datatype and have some 
converters available (import and export).


Definitely worth spending some extra time to make sure that we have 
the data flowing well between each of the different parts/tools, and 
even better to make sure that its done in a way that allows mixing and 
matching with other non-qiime tools.



One thing that we want to avoid is large amounts of manual massaging 
of the automatically generated xml; fixing things up once might not be 
too bad, but having to do it with each new tool version can be 
“frustrating". Although perhaps having a good starting point and only 
needing to manually modify for any updates could be good enough (I’m 
not very familiar with the extent of typical changes between qiime 
versions to make a call on how much changes).





Dan

(resending since I received a message bounce from list)



Daniel Blankenberg 
October 6, 2015 at 9:59 AM
Hi Lance,

I looked at this a bit ago and had similar concerns, particularly with 
the outputs and inputs not being well-defined. In addition to the 
output tar ball —> local, extract —> upload not being great, as you 
mention, the input datatypes, etc, could use some work — in the very 
least, we should definitely create a nice biom datatype and have some 
converters available (import and export).


Definitely worth spending some extra time to make sure that we have 
the data flowing well between each of the different parts/tools, and 
even better to make sure that its done in a way that allows mixing and 
matching with other non-qiime tools.



One thing that we want to avoid is large amounts of manual massaging 
of the automatically generated xml; fixing things up once might not be 
too bad, but having to do it with each new tool version can be 
“frustrating". Although perhaps having a good starting point and only 
needing to manually modify for any updates could be good enough (I’m 
not very familiar with the extent of typical changes between qiime 
versions to make a call on how much changes).





Dan



Lance Parsons 
October 5, 2015 at 5:26 PM
I was recently asked if I could provide a QIIME analysis pipeline for 
16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).


I did a bit of looking around for existing Galaxy wrappers and found 
an application that generates the wrappers for QIIME scripts for 
Galaxy (https://github.com/qiime/qiime-galaxy). This is a very well 
written application that does a great job of wrapping the QIIME 
scripts for Galaxy. However, there are a few things about it that 
don't quite fit my needs.


1. The tools output tgz files of all of the output files. This means 
that to execute a pipeline, the user would have to download the tgz 
files, untar, and then upload whichever file(s) are needed for the 
next step.
2. There is no toolshed repository to install the dependencies for 
these tools, making it a tricky for administrators to automate and 
also maintain various versions of QIIME going forward.
3. There are no toolshed versions of the tools themselves, which also 
makes installation and integration a bit tricky and makes it hard to 
me to create and manage updates, fixes, tweaks, etc. There are also no 
tests, etc.


For these reasons I decided to investigate the feasibility of using 
the generated wrappers as a basis for a "toolshed"

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Daniel Blankenberg]

Hi Lance,

I looked at this a bit ago and had similar concerns, particularly with the 
outputs and inputs not being well-defined. In addition to the output tar ball 
—> local, extract —> upload not being great, as you mention, the input 
datatypes, etc, could use some work — in the very least, we should definitely 
create a nice biom datatype and have some converters available (import and 
export).  

Definitely worth spending some extra time to make sure that we have the data 
flowing well between each of the different parts/tools, and even better to make 
sure that its done in a way that allows mixing and matching with other 
non-qiime tools.


One thing that we want to avoid is large amounts of manual massaging of the 
automatically generated xml; fixing things up once might not be too bad, but 
having to do it with each new tool version can be “frustrating". Although 
perhaps having a good starting point and only needing to manually modify for 
any updates could be good enough (I’m not very familiar with the extent of 
typical changes between qiime versions to make a call on how much changes).




Dan

(resending since I received a message bounce from list)


On Oct 6, 2015, at 9:59 AM, Daniel Blankenberg  wrote:

> Hi Lance,
> 
> I looked at this a bit ago and had similar concerns, particularly with the 
> outputs and inputs not being well-defined. In addition to the output tar ball 
> —> local, extract —> upload not being great, as you mention, the input 
> datatypes, etc, could use some work — in the very least, we should definitely 
> create a nice biom datatype and have some converters available (import and 
> export).  
> 
> Definitely worth spending some extra time to make sure that we have the data 
> flowing well between each of the different parts/tools, and even better to 
> make sure that its done in a way that allows mixing and matching with other 
> non-qiime tools.
> 
> 
> One thing that we want to avoid is large amounts of manual massaging of the 
> automatically generated xml; fixing things up once might not be too bad, but 
> having to do it with each new tool version can be “frustrating". Although 
> perhaps having a good starting point and only needing to manually modify for 
> any updates could be good enough (I’m not very familiar with the extent of 
> typical changes between qiime versions to make a call on how much changes).
> 
> 
> 
> 
> Dan
> 
> 
> On Oct 5, 2015, at 5:26 PM, Lance Parsons  wrote:
> 
>> I was recently asked if I could provide a QIIME analysis pipeline for 16S 
>> data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).
>> 
>> I did a bit of looking around for existing Galaxy wrappers and found an 
>> application that generates the wrappers for QIIME scripts for Galaxy 
>> (https://github.com/qiime/qiime-galaxy). This is a very well written 
>> application that does a great job of wrapping the QIIME scripts for Galaxy. 
>> However, there are a few things about it that don't quite fit my needs.
>> 
>> 1. The tools output tgz files of all of the output files. This means that to 
>> execute a pipeline, the user would have to download the tgz files, untar, 
>> and then upload whichever file(s) are needed for the next step.
>> 2. There is no toolshed repository to install the dependencies for these 
>> tools, making it a tricky for administrators to automate and also maintain 
>> various versions of QIIME going forward.
>> 3. There are no toolshed versions of the tools themselves, which also makes 
>> installation and integration a bit tricky and makes it hard to me to create 
>> and manage updates, fixes, tweaks, etc. There are also no tests, etc.
>> 
>> For these reasons I decided to investigate the feasibility of using the 
>> generated wrappers as a basis for a "toolshed" version of QIIME. If anyone 
>> is interested in helping, or has suggestions, or is working on something 
>> related, I'd be very happy to collaborate.
>> 
>> The repository for the WIP is at 
>> https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There 
>> is also a package on the testtoolshed as well as a first pass at 
>> package_qiime_1_9_1 
>> (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1_9_1).
>> 
>> -- 
>> Lance Parsons - Scientific Programmer
>> 134 Carl C. Icahn Laboratory
>> Lewis-Sigler Institute for Integrative Genomics
>> Princeton University
>> 
>> ___
>> 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:
>> https://lists.galaxyproject.org/
>> 
>> 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 Gal

[galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

[Lance Parsons]

I was recently asked if I could provide a QIIME analysis pipeline for 
16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/).


I did a bit of looking around for existing Galaxy wrappers and found an 
application that generates the wrappers for QIIME scripts for Galaxy 
(https://github.com/qiime/qiime-galaxy). This is a very well written 
application that does a great job of wrapping the QIIME scripts for 
Galaxy. However, there are a few things about it that don't quite fit my 
needs.


1. The tools output tgz files of all of the output files. This means 
that to execute a pipeline, the user would have to download the tgz 
files, untar, and then upload whichever file(s) are needed for the next 
step.
2. There is no toolshed repository to install the dependencies for these 
tools, making it a tricky for administrators to automate and also 
maintain various versions of QIIME going forward.
3. There are no toolshed versions of the tools themselves, which also 
makes installation and integration a bit tricky and makes it hard to me 
to create and manage updates, fixes, tweaks, etc. There are also no 
tests, etc.


For these reasons I decided to investigate the feasibility of using the 
generated wrappers as a basis for a "toolshed" version of QIIME. If 
anyone is interested in helping, or has suggestions, or is working on 
something related, I'd be very happy to collaborate.


The repository for the WIP is at 
https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. 
There is also a package on the testtoolshed as well as a first pass at 
package_qiime_1_9_1 
(https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_1_9_1).


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University

___
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:
 https://lists.galaxyproject.org/

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