Potential Hackathon proposal: RADSeq
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
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/
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@gmail.com> À: "Tiago Antao" <tra@popgen.net>, "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>, "galaxy-iuc" <galaxy-iuc@lists.bx.psu.edu> 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@irisa.fr
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@irisa.fr> 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@gmail.com> À: "Tiago Antao" <tra@popgen.net>, "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>, "galaxy-iuc" <galaxy-iuc@lists.bx.psu.edu> 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@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/
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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 <yvan.le_bras@irisa.fr> 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@gmail.com> À: "Tiago Antao" <tra@popgen.net>, "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>, "galaxy-iuc" <galaxy-iuc@lists.bx.psu.edu> 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@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@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
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@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 ------------------------------------------------------------------
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@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@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--------------------------------------------------...
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 <lecorguille@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@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--------------------------------------------------...
-- ----------------------------------------------------------------- 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
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/
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?
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/
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-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
Hi Shane, please allow me to jump in late - since you are looking for a simple solution: why not rely just on the built in job scheduler? Have a look at ~/config/job_conf.xml.sample_advanced Even on a single box, you can set up different queues with individual restrictions. Hans-Rudolf On 11/24/2015 06:48 PM, Eric Rasche wrote:
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?
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/
Hi Hans-Rudolph, I am grateful to you (and all the other people who share their knowledge on this list) for pointing out a ready made, in-built solution to what I perceived as a problem. Many thanks, Shane
Hi Shane,
please allow me to jump in late - since you are looking for a simple solution: why not rely just on the built in job scheduler? Have a look at ~/config/job_conf.xml.sample_advanced
Even on a single box, you can set up different queues with individual restrictions.
Hans-Rudolf
On 11/24/2015 06:48 PM, Eric Rasche wrote:
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?
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/
On Tue, 24 Nov 2015 10:38:05 +0100 mabernard <mabernard@jouy.inra.fr> 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
Am 24.11.2015 um 20:36 schrieb Tiago Antao:
On Tue, 24 Nov 2015 10:38:05 +0100 mabernard <mabernard@jouy.inra.fr> 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/
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
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
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@gmail.com> a écrit :
Am 24.11.2015 um 20:36 schrieb Tiago Antao:
On Tue, 24 Nov 2015 10:38:05 +0100 mabernard <mabernard@jouy.inra.fr> 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/
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Sorry, I answer too quickly. 2 days are a good duration, not too short and easy to schedule. M mabernard <mabernard@jouy.inra.fr> 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 <bjoern.gruening@gmail.com> a écrit :
Am 24.11.2015 um 20:36 schrieb Tiago Antao:
On Tue, 24 Nov 2015 10:38:05 +0100 mabernard <mabernard@jouy.inra.fr> 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, 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 <mabernard@jouy.inra.fr> 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 <bjoern.gruening@gmail.com> a écrit :
Am 24.11.2015 um 20:36 schrieb Tiago Antao:
On Tue, 24 Nov 2015 10:38:05 +0100 mabernard <mabernard@jouy.inra.fr> 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/
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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@gmail.com> À: "Tiago Antao" <tra@popgen.net>, "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>, "galaxy-iuc" <galaxy-iuc@lists.bx.psu.edu> 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/
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" <bjoern.gruening@gmail.com> À: "Tiago Antao" <tra@popgen.net>, "galaxy-dev" <galaxy-dev@lists.galaxyproject.org>, "galaxy-iuc" <galaxy-iuc@lists.bx.psu.edu> 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/
Ciao, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
On Mon, 23 Nov 2015 12:08:17 -0600 Eric Rasche <esr@tamu.edu> 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
Am 23.11.2015 um 20:56 schrieb Tiago Antao:
On Mon, 23 Nov 2015 12:08:17 -0600 Eric Rasche <esr@tamu.edu> 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
Am 23.11.2015 um 20:51 schrieb Tiago Antao:
On Mon, 23 Nov 2015 18:55:22 +0100 (CET) Yvan Le Bras <yvan.le_bras@irisa.fr> 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!
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 <bjoern.gruening@gmail.com> Date : 23/11/2015 21:28 (GMT+01:00) À : Tiago Antao <tra@popgen.net>, Yvan Le Bras <yvan.le_bras@irisa.fr> Cc : Björn Grüning <bjoern.gruening@gmail.com>, galaxy-dev <galaxy-dev@lists.galaxyproject.org>, galaxy-iuc <galaxy-iuc@lists.bx.psu.edu>, Anthony Bretaudeau <anthony.bretaudeau@inria.fr>, Gildas Le Corguillé <lecorguille@sb-roscoff.fr>, Maria <maria.bernard@jouy.inra.fr> 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 <yvan.le_bras@irisa.fr> 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!
Hi, I have now drafted the issue: https://github.com/galaxyproject/tools-iuc/issues/422 Comments/feedback most appreciated...
participants (9)
-
Björn Grüning -
Eric Rasche -
Gildas Le Corguillé -
Hans-Rudolf Hotz -
John Chilton -
mabernard -
Shane Kelly -
Tiago Antao -
Yvan Le Bras