Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

Hi,

I have now drafted the issue:
https://github.com/galaxyproject/tools-iuc/issues/422

Comments/feedback most appreciated...
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[mabernard]

 Hi,

7th and 8th would be great for me. But I agree with Björn, a github issue
to share our ideas and a doodle is a better way to fixe it.

Have a nice day

Maria

Björn Grüning  a écrit :


Am 24.11.2015 um 20:36 schrieb Tiago Antao:

On Tue, 24 Nov 2015 10:38:05 +0100
mabernard  wrote:


So I'm in to  but not at the date you propose  sorry.
Is the possible the week before (between 7th and 11th) or 2 weeks
later (between 29th to 1st)?


What about the 7th and 8th (March)?


What about a github issue and a doodle link?


Is this OK for everybody?

Thanks,
Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[mabernard]

 Sorry, I answer too quickly.

2 days are a good duration, not too short and easy to schedule.

M

mabernard  a écrit :


Hi,

7th and 8th would be great for me. But I agree with Björn, a github
issue to share our ideas and a doodle is a better way to fixe it.

Have a nice day

Maria

Björn Grüning  a écrit :


Am 24.11.2015 um 20:36 schrieb Tiago Antao:


On Tue, 24 Nov 2015 10:38:05 +0100
mabernard  wrote:


So I'm in to  but not at the date you propose  sorry.
Is the possible the week before (between 7th and 11th) or 2 weeks
later (between 29th to 1st)?


What about the 7th and 8th (March)?


What about a github issue and a doodle link?


Is this OK for everybody?

Thanks,
Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

Hi,

The doodle is available here:
http://doodle.com/poll/hcc83a4yzgnecq4w

The issue will be out soon...


On Wed, 25 Nov 2015 09:05:23 +0100
mabernard  wrote:

>   Hi,
> 
> 7th and 8th would be great for me. But I agree with Björn, a github
> issue to share our ideas and a doodle is a better way to fixe it.
> 
> Have a nice day
> 
> Maria
> 
> Björn Grüning  a écrit :
> 
> > Am 24.11.2015 um 20:36 schrieb Tiago Antao:
> >> On Tue, 24 Nov 2015 10:38:05 +0100
> >> mabernard  wrote:
> >>
> >>> So I'm in to  but not at the date you propose  sorry.
> >>> Is the possible the week before (between 7th and 11th) or 2 weeks
> >>> later (between 29th to 1st)?
> >>
> >> What about the 7th and 8th (March)?
> >
> > What about a github issue and a doodle link?
> >
> >> Is this OK for everybody?
> >>
> >> Thanks,
> >> Tiago
> >> ___
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> >
> >  

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Am 24.11.2015 um 21:02 schrieb Tiago Antao:
>> What about a github issue and a doodle link?
> 
> I want to contact a couple of people before the github issue. That will
> be ready tomorrow.
> 
> WRT doodle, a question: do you folks think 2 days is the correct
> duration? I do not have an opinion myself, but is that a sensible
> default (as the metagenomics one)?

I don't think I will be able to get more free time than 2 days.
Anyway, I think the codefest is an ideal place to kick-start this effort
to get the right people together and create a few PR. Reviewing and
working further on it can happen later.

> Tiago
> 
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

> What about a github issue and a doodle link?

I want to contact a couple of people before the github issue. That will
be ready tomorrow.

WRT doodle, a question: do you folks think 2 days is the correct
duration? I do not have an opinion myself, but is that a sensible
default (as the metagenomics one)?

Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Am 24.11.2015 um 20:36 schrieb Tiago Antao:
> On Tue, 24 Nov 2015 10:38:05 +0100
> mabernard  wrote:
> 
>> So I'm in to  but not at the date you propose  sorry.
>> Is the possible the week before (between 7th and 11th) or 2 weeks
>> later (between 29th to 1st)?
> 
> What about the 7th and 8th (March)?

What about a github issue and a doodle link?

> Is this OK for everybody?
> 
> 
> Thanks,
> Tiago
> ___
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

On Tue, 24 Nov 2015 10:38:05 +0100
mabernard  wrote:

> So I'm in to  but not at the date you propose  sorry.
> Is the possible the week before (between 7th and 11th) or 2 weeks
> later (between 29th to 1st)?

What about the 7th and 8th (March)?

Is this OK for everybody?


Thanks,
Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[mabernard]

 Dear all,

I work on many RADSeq projects, and I'm using Stacks for doing this. I
developpe(d) some scripts to describe the result, compute descriptive
statistics 

So I'm really interested to participate to this Hackathon, to give autonomy
to biologist.

So I'm in to  but not at the date you propose  sorry.
Is the possible the week before (between 7th and 11th) or 2 weeks later
(between 29th to 1st)?

Have a nice day

Maria

Gildas Le Corguillé  a écrit :


Hi All,

I have some knowledges about RADSeq ... at least about the
bioinformatics part. This technology is growing up in my lab (marine
science) and I'm involve in few of those projects.

So I'm in!

Gildas

Le 23/11/2015 20:59, Tiago Antao a écrit :

On Mon, 23 Nov 2015 18:03:05 +
John Chilton  wrote:


Someone should create an tools-iuc issue for this, I will certainly
participate also. I don't know anything RADSeq (or really much about
any kind of Seq) but I suspect I can find a way to help if there is a
TODO or ideas list that is tracked on github.


I am surrounded by RADSeq specialists (including some of the people
that developed the technology).
I will contact them to get a list of things needed (TODO) and probably
try to convince one of them to introduce the technology.
Unfortunately the geekiest of them all is not a big Galaxy fan, I am
afraid.

Tiago
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--
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81


http://abims.sb-roscoff.fr--
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Gildas Le Corguillé]

The same for me, I have another Hackathon ^^' the 14-16th of march.

Anyway, I can take part through the GitHUB.

Gildas


Le 24/11/2015 10:38, mabernard a écrit :


Dear all,

I work on many RADSeq projects, and I'm using Stacks for doing this. I 
developpe(d) some scripts to describe the result, compute descriptive 
statistics 


So I'm really interested to participate to this Hackathon, to give 
autonomy to biologist.


So I'm in to  but not at the date you propose  sorry.
Is the possible the week before (between 7th and 11th) or 2 weeks 
later (between 29th to 1st)?


Have a nice day

Maria

Gildas Le Corguillé > a écrit :



Hi All,

I have some knowledges about RADSeq ... at least about the 
bioinformatics part. This technology is growing up in my lab (marine 
science) and I'm involve in few of those projects.


So I'm in!

Gildas



Le 23/11/2015 20:59, Tiago Antao a écrit :


On Mon, 23 Nov 2015 18:03:05 +
John Chilton mailto:jmchil...@gmail.com>> wrote:


Someone should create an tools-iuc issue for this, I will certainly
participate also. I don't know anything RADSeq (or really much about
any kind of Seq) but I suspect I can find a way to help if there is a
TODO or ideas list that is tracked on github.


I am surrounded by RADSeq specialists (including some of the people
that developed the technology).
I will contact them to get a list of things needed (TODO) and probably
try to convince one of them to introduce the technology.
Unfortunately the geekiest of them all is not a big Galaxy fan, I am
afraid.

Tiago
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--
-
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Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr--






--
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Gildas Le Corguillé]

Hi All,

I have some knowledges about RADSeq ... at least about the 
bioinformatics part. This technology is growing up in my lab (marine 
science) and I'm involve in few of those projects.


So I'm in!

Gildas



Le 23/11/2015 20:59, Tiago Antao a écrit :

On Mon, 23 Nov 2015 18:03:05 +
John Chilton  wrote:


Someone should create an tools-iuc issue for this, I will certainly
participate also. I don't know anything RADSeq (or really much about
any kind of Seq) but I suspect I can find a way to help if there is a
TODO or ideas list that is tracked on github.


I am surrounded by RADSeq specialists (including some of the people
that developed the technology).
I will contact them to get a list of things needed (TODO) and probably
try to convince one of them to introduce the technology.
Unfortunately the geekiest of them all is not a big Galaxy fan, I am
afraid.

Tiago
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--
-
Gildas Le Corguillé - Bioinformatician/Bioanalyste
Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
http://abims.sb-roscoff.fr
--

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Am 23.11.2015 um 20:51 schrieb Tiago Antao:
> On Mon, 23 Nov 2015 18:55:22 +0100 (CET)
> Yvan Le Bras  wrote:
> 
> 
>> So ready to go further with a remote hackathon. Maybe on March or
>> April 2016 ?
> 
> What about, tentatively, 14 and 15 of March? That is a Monday and a
> Tuesday...

Sounds good to me!

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Am 23.11.2015 um 20:56 schrieb Tiago Antao:
> On Mon, 23 Nov 2015 12:08:17 -0600
> Eric Rasche  wrote:
> 
>> Maybe you all would consider doing something akin to Marten's mention
>> of the Jenkins hackathons where they have short (10-30 minute)
>> seminars on background information related to the area so that the
>> more experienced volunteers can better help out the newcomers?
> 
> Depending on the audience, we might need 2 types of intros:
> RADSeq to Galaxy developers
> Galaxy development to RADSeqers.

I no one else steps up, I can do this one.

> 
> Tiago
> 
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Yvan Le Bras]

Hi everyone, 
Thanks Tiago for this proposal and for proposing these days. Sounds good to me 
to. I have some teaching material  I used on training sessions 
(https://www.e-biogenouest.org/resources/1321) if this can be of interest... I 
can try to englishize it ;)
Cheers,
Yvan 

Envoyé depuis le réseau SFR

 Message d'origine 
De : Björn Grüning  
Date : 23/11/2015  21:28  (GMT+01:00) 
À : Tiago Antao , Yvan Le Bras  
Cc : Björn Grüning , galaxy-dev 
, galaxy-iuc , 
Anthony Bretaudeau , Gildas Le Corguillé 
, Maria  
Objet : Re: [galaxy-dev] Potential Hackathon proposal: RADSeq 



Am 23.11.2015 um 20:51 schrieb Tiago Antao:
> On Mon, 23 Nov 2015 18:55:22 +0100 (CET)
> Yvan Le Bras  wrote:
> 
> 
>> So ready to go further with a remote hackathon. Maybe on March or
>> April 2016 ?
> 
> What about, tentatively, 14 and 15 of March? That is a Monday and a
> Tuesday...

Sounds good to me!

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

On Mon, 23 Nov 2015 18:03:05 +
John Chilton  wrote:

> Someone should create an tools-iuc issue for this, I will certainly
> participate also. I don't know anything RADSeq (or really much about
> any kind of Seq) but I suspect I can find a way to help if there is a
> TODO or ideas list that is tracked on github.


I am surrounded by RADSeq specialists (including some of the people
that developed the technology).
I will contact them to get a list of things needed (TODO) and probably
try to convince one of them to introduce the technology.
Unfortunately the geekiest of them all is not a big Galaxy fan, I am
afraid.

Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

On Mon, 23 Nov 2015 12:08:17 -0600
Eric Rasche  wrote:

> Maybe you all would consider doing something akin to Marten's mention
> of the Jenkins hackathons where they have short (10-30 minute)
> seminars on background information related to the area so that the
> more experienced volunteers can better help out the newcomers?

Depending on the audience, we might need 2 types of intros:
RADSeq to Galaxy developers
Galaxy development to RADSeqers.

Tiago
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

On Mon, 23 Nov 2015 18:55:22 +0100 (CET)
Yvan Le Bras  wrote:


> So ready to go further with a remote hackathon. Maybe on March or
> April 2016 ?

What about, tentatively, 14 and 15 of March? That is a Monday and a
Tuesday...
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Am 23.11.2015 um 19:03 schrieb John Chilton:
> Someone should create an tools-iuc issue for this, I will certainly
> participate also. I don't know anything RADSeq (or really much about
> any kind of Seq) but I suspect I can find a way to help if there is a
> TODO or ideas list that is tracked on github.

Tiago, if you like please create such an issue. For inspiration please
look at this one :)
https://github.com/galaxyproject/tools-iuc/issues/299

Thanks,
Bjoern


> Thanks all,
> -John
> 
> On Mon, Nov 23, 2015 at 5:55 PM, Yvan Le Bras  wrote:
>> Hi Tiago, Björn,
>>
>> I'm strongly interested by a RADseq hackathon! I begin to exchange with some 
>> colleagues (Cced), indeed there will be at least 2 others french labs 
>> interested. Maria have developped some scripts for STACKS, and putting it on 
>> the Galaxy will be cool. Here, we have developped a recent update of our 
>> Stacks descriptors and wrappers, Anthony & us think that it can be 
>> interesting to try using Interactive Environment to propose the use of the 
>> Stacks webinterface + database to correct haplotypes.. or not ;) 
>> Furthermore, we begin using other pipelines as Ddocent and it will be cool 
>> to put it on Galaxy
>>
>> So ready to go further with a remote hackathon. Maybe on March or April 2016 
>> ?
>>
>> Wishing you the best.
>>
>> Cheers,
>> Yvan
>>
>> - Mail original -
>>> De: "Björn Grüning" 
>>> À: "Tiago Antao" , "galaxy-dev" 
>>> , "galaxy-iuc"
>>> 
>>> Envoyé: Lundi 23 Novembre 2015 17:52:35
>>> Objet: Re: [galaxy-dev] Potential Hackathon proposal: RADSeq
>>>
>>> Hi Tiago,
>>>
>>> I like this idea very much and I will try to help as much as I can.
>>>
>>> I hope someone else will join otherwise I will be in for a tandem hack :)
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> Am 16.11.2015 um 17:05 schrieb Tiago Antao:
>>>> Dear all,
>>>>
>>>> This is an email to inquire about the potential community interest in
>>>> having a RADSeq hackathon.
>>>>
>>>> There has been quite some interest in analyzing RADSeq with Galaxy. As
>>>> far as I know there are essentially only two tools dedicated to this,
>>>> wrapping stacks and prada.
>>>>
>>>> I have been exchanging emails with the authors of the stacks tool (Yvan
>>>> is Cced here) and they seem to have interest in pursuing this also.
>>>>
>>>> Where I am based now, we have quite a few RADSeq users that can advise
>>>> on needs of the RADSeq community (obviously if others have any ideas,
>>>> those would be most welcome).
>>>>
>>>> We also have good connections to some of the researchers involved with
>>>> creating the technology, whom I believe could provide some advice on
>>>> what we need to implement.
>>>>
>>>> RADSeq is a cheap sequencing technology that is used by many
>>>> resource-limited groups and they would potentially benefit a lot from
>>>> easy-to-use galaxy tools.
>>>>
>>>> Any interest in this?
>>>>
>>>> Tiago
>>>> ___
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>>>>
>>> ___
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>>
>> --
>> -
>> Yvan Le Bras, PhD @Yvan2935 <°><
>> e-Biogenouest project http://www.e-biogenouest.org
>> CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex
>> tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51
>> yvan.le_b...@irisa.fr
>>
>> ___
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Eric Rasche]

Knowing nothing about RADseq...

Maybe you all would consider doing something akin to Marten's mention of the 
Jenkins hackathons where they have short (10-30 minute) seminars on background 
information related to the area so that the more experienced volunteers can 
better help out the newcomers?


On 11/23/2015 12:05 PM, Björn Grüning wrote:
> Yvan, this sounds great!
>
> I think it's up to Tiago to pick a date :)
>
> Am 23.11.2015 um 18:55 schrieb Yvan Le Bras:
> > Hi Tiago, Björn,
> >
> > I'm strongly interested by a RADseq hackathon! I begin to exchange
> > with some colleagues (Cced), indeed there will be at least 2 others
> > french labs interested. Maria have developped some scripts for
> > STACKS, and putting it on the Galaxy will be cool. Here, we have
> > developped a recent update of our Stacks descriptors and wrappers,
> > Anthony & us think that it can be interesting to try using
> > Interactive Environment
>
> Sweet! Have a look at this document were I collected some ideas how this
> could work:
>
> https://gist.github.com/bgruening/4414529ff0d951f94ef6
>
> > to propose the use of the Stacks webinterface
> > + database to correct haplotypes.. or not ;) Furthermore, we
> > begin using other pipelines as Ddocent and it will be cool to put it
> > on Galaxy
> >
> > So ready to go further with a remote hackathon. Maybe on March or
> > April 2016 ?
>
> I will leave this decision to Tiago :)
> But this all sounds very interesting!
>
> Cheers,
> Bjoern
>
> > Wishing you the best.
> >
> > Cheers, Yvan
> >
> > - Mail original -
> >> De: "Björn Grüning"  À: "Tiago Antao"
> >> , "galaxy-dev"
> >> , "galaxy-iuc"
> >>  Envoyé: Lundi 23 Novembre 2015
> >> 17:52:35 Objet: Re: [galaxy-dev] Potential Hackathon proposal:
> >> RADSeq
> >>
> >> Hi Tiago,
> >>
> >> I like this idea very much and I will try to help as much as I
> >> can.
> >>
> >> I hope someone else will join otherwise I will be in for a tandem
> >> hack :)
> >>
> >> Cheers, Bjoern
> >>
> >> Am 16.11.2015 um 17:05 schrieb Tiago Antao:
> >>> Dear all,
> >>>
> >>> This is an email to inquire about the potential community
> >>> interest in having a RADSeq hackathon.
> >>>
> >>> There has been quite some interest in analyzing RADSeq with
> >>> Galaxy. As far as I know there are essentially only two tools
> >>> dedicated to this, wrapping stacks and prada.
> >>>
> >>> I have been exchanging emails with the authors of the stacks tool
> >>> (Yvan is Cced here) and they seem to have interest in pursuing
> >>> this also.
> >>>
> >>> Where I am based now, we have quite a few RADSeq users that can
> >>> advise on needs of the RADSeq community (obviously if others have
> >>> any ideas, those would be most welcome).
> >>>
> >>> We also have good connections to some of the researchers involved
> >>> with creating the technology, whom I believe could provide some
> >>> advice on what we need to implement.
> >>>
> >>> RADSeq is a cheap sequencing technology that is used by many
> >>> resource-limited groups and they would potentially benefit a lot
> >>> from easy-to-use galaxy tools.
> >>>
> >>> Any interest in this?
> >>>
> >>> Tiago
> >>> ___
> >>> 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 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 Galaxy lists, please use the interface at:
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>
Ciao,
Eric

-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Yvan, this sounds great!

I think it's up to Tiago to pick a date :)

Am 23.11.2015 um 18:55 schrieb Yvan Le Bras:
> Hi Tiago, Björn,
> 
> I'm strongly interested by a RADseq hackathon! I begin to exchange
> with some colleagues (Cced), indeed there will be at least 2 others
> french labs interested. Maria have developped some scripts for
> STACKS, and putting it on the Galaxy will be cool. Here, we have
> developped a recent update of our Stacks descriptors and wrappers,
> Anthony & us think that it can be interesting to try using
> Interactive Environment 

Sweet! Have a look at this document were I collected some ideas how this
could work:

https://gist.github.com/bgruening/4414529ff0d951f94ef6

> to propose the use of the Stacks webinterface
> + database to correct haplotypes.. or not ;) Furthermore, we
> begin using other pipelines as Ddocent and it will be cool to put it
> on Galaxy
> 
> So ready to go further with a remote hackathon. Maybe on March or
> April 2016 ?

I will leave this decision to Tiago :)
But this all sounds very interesting!

Cheers,
Bjoern

> Wishing you the best.
> 
> Cheers, Yvan
> 
> - Mail original -
>> De: "Björn Grüning"  À: "Tiago Antao"
>> , "galaxy-dev"
>> , "galaxy-iuc" 
>>  Envoyé: Lundi 23 Novembre 2015
>> 17:52:35 Objet: Re: [galaxy-dev] Potential Hackathon proposal:
>> RADSeq
>> 
>> Hi Tiago,
>> 
>> I like this idea very much and I will try to help as much as I
>> can.
>> 
>> I hope someone else will join otherwise I will be in for a tandem
>> hack :)
>> 
>> Cheers, Bjoern
>> 
>> Am 16.11.2015 um 17:05 schrieb Tiago Antao:
>>> Dear all,
>>> 
>>> This is an email to inquire about the potential community
>>> interest in having a RADSeq hackathon.
>>> 
>>> There has been quite some interest in analyzing RADSeq with
>>> Galaxy. As far as I know there are essentially only two tools
>>> dedicated to this, wrapping stacks and prada.
>>> 
>>> I have been exchanging emails with the authors of the stacks tool
>>> (Yvan is Cced here) and they seem to have interest in pursuing
>>> this also.
>>> 
>>> Where I am based now, we have quite a few RADSeq users that can
>>> advise on needs of the RADSeq community (obviously if others have
>>> any ideas, those would be most welcome).
>>> 
>>> We also have good connections to some of the researchers involved
>>> with creating the technology, whom I believe could provide some
>>> advice on what we need to implement.
>>> 
>>> RADSeq is a cheap sequencing technology that is used by many 
>>> resource-limited groups and they would potentially benefit a lot
>>> from easy-to-use galaxy tools.
>>> 
>>> Any interest in this?
>>> 
>>> Tiago 
>>> ___ 
>>> 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 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/
> 
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[John Chilton]

Someone should create an tools-iuc issue for this, I will certainly
participate also. I don't know anything RADSeq (or really much about
any kind of Seq) but I suspect I can find a way to help if there is a
TODO or ideas list that is tracked on github.

Thanks all,
-John

On Mon, Nov 23, 2015 at 5:55 PM, Yvan Le Bras  wrote:
> Hi Tiago, Björn,
>
> I'm strongly interested by a RADseq hackathon! I begin to exchange with some 
> colleagues (Cced), indeed there will be at least 2 others french labs 
> interested. Maria have developped some scripts for STACKS, and putting it on 
> the Galaxy will be cool. Here, we have developped a recent update of our 
> Stacks descriptors and wrappers, Anthony & us think that it can be 
> interesting to try using Interactive Environment to propose the use of the 
> Stacks webinterface + database to correct haplotypes.. or not ;) 
> Furthermore, we begin using other pipelines as Ddocent and it will be cool to 
> put it on Galaxy
>
> So ready to go further with a remote hackathon. Maybe on March or April 2016 ?
>
> Wishing you the best.
>
> Cheers,
> Yvan
>
> - Mail original -
>> De: "Björn Grüning" 
>> À: "Tiago Antao" , "galaxy-dev" 
>> , "galaxy-iuc"
>> 
>> Envoyé: Lundi 23 Novembre 2015 17:52:35
>> Objet: Re: [galaxy-dev] Potential Hackathon proposal: RADSeq
>>
>> Hi Tiago,
>>
>> I like this idea very much and I will try to help as much as I can.
>>
>> I hope someone else will join otherwise I will be in for a tandem hack :)
>>
>> Cheers,
>> Bjoern
>>
>> Am 16.11.2015 um 17:05 schrieb Tiago Antao:
>> > Dear all,
>> >
>> > This is an email to inquire about the potential community interest in
>> > having a RADSeq hackathon.
>> >
>> > There has been quite some interest in analyzing RADSeq with Galaxy. As
>> > far as I know there are essentially only two tools dedicated to this,
>> > wrapping stacks and prada.
>> >
>> > I have been exchanging emails with the authors of the stacks tool (Yvan
>> > is Cced here) and they seem to have interest in pursuing this also.
>> >
>> > Where I am based now, we have quite a few RADSeq users that can advise
>> > on needs of the RADSeq community (obviously if others have any ideas,
>> > those would be most welcome).
>> >
>> > We also have good connections to some of the researchers involved with
>> > creating the technology, whom I believe could provide some advice on
>> > what we need to implement.
>> >
>> > RADSeq is a cheap sequencing technology that is used by many
>> > resource-limited groups and they would potentially benefit a lot from
>> > easy-to-use galaxy tools.
>> >
>> > Any interest in this?
>> >
>> > Tiago
>> > ___
>> > 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 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/
>
> --
> -
> Yvan Le Bras, PhD @Yvan2935 <°><
> e-Biogenouest project http://www.e-biogenouest.org
> CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex
> tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51
> yvan.le_b...@irisa.fr
>
> ___
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> and other Galaxy lists, please use the interface at:
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>
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>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Yvan Le Bras]

Hi Tiago, Björn,

I'm strongly interested by a RADseq hackathon! I begin to exchange with some 
colleagues (Cced), indeed there will be at least 2 others french labs 
interested. Maria have developped some scripts for STACKS, and putting it on 
the Galaxy will be cool. Here, we have developped a recent update of our Stacks 
descriptors and wrappers, Anthony & us think that it can be interesting to try 
using Interactive Environment to propose the use of the Stacks webinterface + 
database to correct haplotypes.. or not ;) Furthermore, we begin using 
other pipelines as Ddocent and it will be cool to put it on Galaxy

So ready to go further with a remote hackathon. Maybe on March or April 2016 ?

Wishing you the best.

Cheers,
Yvan

- Mail original -
> De: "Björn Grüning" 
> À: "Tiago Antao" , "galaxy-dev" 
> , "galaxy-iuc"
> 
> Envoyé: Lundi 23 Novembre 2015 17:52:35
> Objet: Re: [galaxy-dev] Potential Hackathon proposal: RADSeq
> 
> Hi Tiago,
> 
> I like this idea very much and I will try to help as much as I can.
> 
> I hope someone else will join otherwise I will be in for a tandem hack :)
> 
> Cheers,
> Bjoern
> 
> Am 16.11.2015 um 17:05 schrieb Tiago Antao:
> > Dear all,
> > 
> > This is an email to inquire about the potential community interest in
> > having a RADSeq hackathon.
> > 
> > There has been quite some interest in analyzing RADSeq with Galaxy. As
> > far as I know there are essentially only two tools dedicated to this,
> > wrapping stacks and prada.
> > 
> > I have been exchanging emails with the authors of the stacks tool (Yvan
> > is Cced here) and they seem to have interest in pursuing this also.
> > 
> > Where I am based now, we have quite a few RADSeq users that can advise
> > on needs of the RADSeq community (obviously if others have any ideas,
> > those would be most welcome).
> > 
> > We also have good connections to some of the researchers involved with
> > creating the technology, whom I believe could provide some advice on
> > what we need to implement.
> > 
> > RADSeq is a cheap sequencing technology that is used by many
> > resource-limited groups and they would potentially benefit a lot from
> > easy-to-use galaxy tools.
> > 
> > Any interest in this?
> > 
> > Tiago
> > ___
> > 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 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/

-- 
-
 
Yvan Le Bras, PhD @Yvan2935 <°>< 
e-Biogenouest project http://www.e-biogenouest.org 
CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex 
tél.: +33 (0) 2 99 84 71 79 / +33 (0) 6.10.43.96.51 
yvan.le_b...@irisa.fr 

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Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

[Björn Grüning]

Hi Tiago,

I like this idea very much and I will try to help as much as I can.

I hope someone else will join otherwise I will be in for a tandem hack :)

Cheers,
Bjoern

Am 16.11.2015 um 17:05 schrieb Tiago Antao:
> Dear all,
> 
> This is an email to inquire about the potential community interest in
> having a RADSeq hackathon.
> 
> There has been quite some interest in analyzing RADSeq with Galaxy. As
> far as I know there are essentially only two tools dedicated to this,
> wrapping stacks and prada.
> 
> I have been exchanging emails with the authors of the stacks tool (Yvan
> is Cced here) and they seem to have interest in pursuing this also.
> 
> Where I am based now, we have quite a few RADSeq users that can advise
> on needs of the RADSeq community (obviously if others have any ideas,
> those would be most welcome).
> 
> We also have good connections to some of the researchers involved with
> creating the technology, whom I believe could provide some advice on
> what we need to implement.
> 
> RADSeq is a cheap sequencing technology that is used by many
> resource-limited groups and they would potentially benefit a lot from
> easy-to-use galaxy tools.
> 
> Any interest in this?
> 
> Tiago
> ___
> 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/
> 
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[galaxy-dev] Potential Hackathon proposal: RADSeq

[Tiago Antao]

Dear all,

This is an email to inquire about the potential community interest in
having a RADSeq hackathon.

There has been quite some interest in analyzing RADSeq with Galaxy. As
far as I know there are essentially only two tools dedicated to this,
wrapping stacks and prada.

I have been exchanging emails with the authors of the stacks tool (Yvan
is Cced here) and they seem to have interest in pursuing this also.

Where I am based now, we have quite a few RADSeq users that can advise
on needs of the RADSeq community (obviously if others have any ideas,
those would be most welcome).

We also have good connections to some of the researchers involved with
creating the technology, whom I believe could provide some advice on
what we need to implement.

RADSeq is a cheap sequencing technology that is used by many
resource-limited groups and they would potentially benefit a lot from
easy-to-use galaxy tools.

Any interest in this?

Tiago
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