De: "Björn Grüning" <bjoern.gruening(a)gmail.com&gt; À: "Tiago Antao" <tra(a)popgen.net&gt;, "galaxy-dev" <galaxy-dev(a)lists.galaxyproject.org&gt;, "galaxy-iuc" <galaxy-iuc(a)lists.bx.psu.edu&gt; 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/

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 <yvan.le_bras(a)irisa.fr&gt; 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" <bjoern.gruening(a)gmail.com&gt; >> À: "Tiago Antao" <tra(a)popgen.net&gt;, "galaxy-dev" <galaxy-dev(a)lists.galaxyproject.org&gt;, "galaxy-iuc" >> <galaxy-iuc(a)lists.bx.psu.edu&gt; >> 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_bras(a)irisa.fr > > ___________________________________________________________ > 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/

On Mon, 23 Nov 2015 18:03:05 +0000 John Chilton <jmchilton(a)gmail.com&gt; 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 ___________________________________________________________ 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/

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 <lecorguille(a)sb-roscoff.fr <mailto:lecorguille@sb-roscoff.fr>> 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 +0000 >> John Chilton <jmchilton(a)gmail.com <mailto:jmchilton@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 >> ___________________________________________________________ >> 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/ > -- > ----------------------------------------------------------------- > 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-----------------------------------------------...

Hi, I am looking for a simple task scheduler to use with Galaxy and initially picked Torque, but since my server is a single box, Torque would appear to be overkill? Can I have any input from anyone who may have used it? Thanks for any response ___________________________________________________________ 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/

I'd also recommend HTCondor. Very easy to set up on debian/ubuntu, apt-get has a quick questionnaire that gets you up and running. Cheers, Eric On 11/24/2015 11:46 AM, Björn Grüning wrote: > Hi Shane, > > would Slurm work for you? > > http://slurm.schedmd.com/ > > Cheers, > Bjoern > > Am 24.11.2015 um 13:12 schrieb Shane Kelly: >> Hi, >> I am looking for a simple task scheduler to use with Galaxy and >> initially picked Torque, but since my server is a single box, Torque >> would appear to be overkill? >> >> Can I have any input from anyone who may have used it? >> >> Thanks for any response >> ___________________________________________________________ >> 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/ >

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 a github issue and a doodle link?

Am 24.11.2015 um 20:36 schrieb Tiago Antao: > On Tue, 24 Nov 2015 10:38:05 +0100 > mabernard <mabernard(a)jouy.inra.fr&gt; 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 > ___________________________________________________________ > 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/  

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 <bjoern.gruening(a)gmail.com&gt; a écrit : > Am 24.11.2015 um 20:36 schrieb Tiago Antao: >> On Tue, 24 Nov 2015 10:38:05 +0100 >> mabernard <mabernard(a)jouy.inra.fr&gt; 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 >> ___________________________________________________________ >> 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, 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" <bjoern.gruening(a)gmail.com&gt; À: "Tiago Antao" >> <tra(a)popgen.net&gt;, "galaxy-dev" >> <galaxy-dev(a)lists.galaxyproject.org&gt;, "galaxy-iuc" >> <galaxy-iuc(a)lists.bx.psu.edu&gt; 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

On Mon, 23 Nov 2015 12:08:17 -0600 Eric Rasche <esr(a)tamu.edu&gt; 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

On Mon, 23 Nov 2015 18:55:22 +0100 (CET) Yvan Le Bras <yvan.le_bras(a)irisa.fr&gt; 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...