Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Bjoern Gruening]

On 15.03.2016 18:11, Léo Biscassi wrote:
Hi, thanks for the considerations in the code, I'll make the changes 
later.
The packages Autodock Vina and MGL Tools works fine!? I saw that tests 
passed with success on Travis.


No, not really. You need to create a .shed.yml file to trigger the tests.
Let's move this discussion to github.

Thanks again!
Bjoern


Cheers,

On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening 
> wrote:


Saw it! Will review it today, this looks really nice!


On 15.03.2016 08:28, Léo Biscassi wrote:

Hi Bjorn, I've created the pull request [1] in your repository. I
will be grateful if you can assist me with the functional tests
on the docking tool and the final validation of the tool
dependencies.

[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi
> wrote:

Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is
that the content of example output is not the same of output
file of test. This is shown by the command diff performed on
planemo test.
Today, I'll create a pull request in your repository for that
we can fix the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning
> wrote:



Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> Hi folks,
> I have make somes alterations on my tools to adjust of
according with
> best pratices of development of tools presented in [1]
[2]. The
> repository of tools was changed for [3].
> I was testing the tool of docking [4] with the command
planemo t, but as
> the algorithm used is heuristic, the output files not
have the same
> content that as output files example and planemo tests
fails. Any
> suggestion to solve this problem?

Is there anything in the file that is the same? Filesize?
Some lines
that are everytime the same (no matter where in the file)?

You could create a PR and I will review it and give you
feedback.
Cheers,
Bjoern


> [1]
>

https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> [2] https://planemo.readthedocs.org/en/latest/
> [3] https://github.com/leobiscassi/autodock_vina_tools
> [4]
>

https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>
> Att.
>
> On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi

> >> wrote:
>
> Hi Bjorn, the branch model of ChemicalToolBoX is
the same presented
> in [1]? Could guide me about it?
>
> [1]
https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>
> Att.
>
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi

> >> wrote:
>
> Ok, thanks!
>
> Best regards,
>
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> 
>>
> wrote:
>
>
>
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional
prototype, its current
> version is able to
> > integrate with projects. In fact, I was
looking for
> projects like
> > ChemicalToolBoX because I would like to
develop my tools
> under project that
> > has more options. In this way,
ChemicalToolBoX is a great
> 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi, thanks for the considerations in the code, I'll make the changes later.
The packages Autodock Vina and MGL Tools works fine!? I saw that tests
passed with success on Travis.

Cheers,

On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening 
wrote:

> Saw it! Will review it today, this looks really nice!
>
>
> On 15.03.2016 08:28, Léo Biscassi wrote:
>
> Hi Bjorn, I've created the pull request [1] in your repository. I will be
> grateful if you can assist me with the functional tests on the docking tool
> and the final validation of the tool dependencies.
>
> [1] https://github.com/bgruening/galaxytools/pull/310
>
> Thanks a lot!
>
> Best regards,
>
> On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi 
> wrote:
>
>> Hi, thanks for the reply.
>> About the branch model, ok! I'll follow the model presented.
>> About the error in planemo functional tests, the problem is that the
>> content of example output is not the same of output file of test. This is
>> shown by the command diff performed on planemo test.
>> Today, I'll create a pull request in your repository for that we can fix
>> the problem.
>> Thank for the helps.
>>
>> I'm excited about this.
>>
>> Best regards,
>>
>>
>>
>> On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
>> wrote:
>>
>>>
>>>
>>> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
>>> > Hi folks,
>>> > I have make somes alterations on my tools to adjust of according with
>>> > best pratices of development of tools presented in [1] [2]. The
>>> > repository of tools was changed for [3].
>>> > I was testing the tool of docking [4] with the command planemo t, but
>>> as
>>> > the algorithm used is heuristic, the output files not have the same
>>> > content that as output files example and planemo tests fails. Any
>>> > suggestion to solve this problem?
>>>
>>> Is there anything in the file that is the same? Filesize? Some lines
>>> that are everytime the same (no matter where in the file)?
>>>
>>> You could create a PR and I will review it and give you feedback.
>>> Cheers,
>>> Bjoern
>>>
>>>
>>> > [1]
>>> >
>>> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
>>> > [2] https://planemo.readthedocs.org/en/latest/
>>> > [3] https://github.com/leobiscassi/autodock_vina_tools
>>> > [4]
>>> >
>>> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>>> >
>>> > Att.
>>> >
>>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi >> > > wrote:
>>> >
>>> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
>>> > in [1]? Could guide me about it?
>>> >
>>> > [1]
>>> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>>> >
>>> > Att.
>>> >
>>> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi <
>>> leo.bisca...@gmail.com
>>> > > wrote:
>>> >
>>> > Ok, thanks!
>>> >
>>> > Best regards,
>>> >
>>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>>> > >
>>> > wrote:
>>> >
>>> >
>>> >
>>> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
>>> > > Hi,
>>> > > Thanks all your attention.
>>> > > Although my project is functional prototype, its current
>>> > version is able to
>>> > > integrate with projects. In fact, I was looking for
>>> > projects like
>>> > > ChemicalToolBoX because I would like to develop my tools
>>> > under project that
>>> > > has more options. In this way, ChemicalToolBoX is a great
>>> > opportunity for
>>> > > me.
>>> > > Can you update the trello card with my project? Is it
>>> > necessary for your
>>> > > organization?
>>> >
>>> > I added you :) So you have all right to modify cards.
>>> > Let me know if you need help with Tool development or git.
>>> >
>>> > This is exciting!
>>> > Cheers,
>>> > Bjoern
>>> >
>>> > > Best regards,
>>> > >
>>> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
>>> > > bjoern.gruen...@gmail.com>>
>>> > > wrote:
>>> > >
>>> > >>
>>> > >>
>>> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>>> > >>> Hi,
>>> > >>>
>>> > >>> I've found this Trello card (
>>> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration
>>> ).
>>> > Do you have more
>>> > >>> information about it?
>>> > >>
>>> > >> Afaik we can not use his work as it was done for some
>>> > company and he
>>> > >> moved on ... so this is unfortunately no option 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Bjoern Gruening]

Saw it! Will review it today, this looks really nice!

On 15.03.2016 08:28, Léo Biscassi wrote:
Hi Bjorn, I've created the pull request [1] in your repository. I will 
be grateful if you can assist me with the functional tests on the 
docking tool and the final validation of the tool dependencies.


[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi > wrote:


Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is that
the content of example output is not the same of output file of
test. This is shown by the command diff performed on planemo test.
Today, I'll create a pull request in your repository for that we
can fix the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning
> wrote:



Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> Hi folks,
> I have make somes alterations on my tools to adjust of
according with
> best pratices of development of tools presented in [1] [2]. The
> repository of tools was changed for [3].
> I was testing the tool of docking [4] with the command
planemo t, but as
> the algorithm used is heuristic, the output files not have
the same
> content that as output files example and planemo tests
fails. Any
> suggestion to solve this problem?

Is there anything in the file that is the same? Filesize? Some
lines
that are everytime the same (no matter where in the file)?

You could create a PR and I will review it and give you feedback.
Cheers,
Bjoern


> [1]
>

https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> [2] https://planemo.readthedocs.org/en/latest/
> [3] https://github.com/leobiscassi/autodock_vina_tools
> [4]
>

https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>
> Att.
>
> On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi

> >> wrote:
>
> Hi Bjorn, the branch model of ChemicalToolBoX is the
same presented
> in [1]? Could guide me about it?
>
> [1]
https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>
> Att.
>
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi

> >> wrote:
>
> Ok, thanks!
>
> Best regards,
>
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> 
>>
> wrote:
>
>
>
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional prototype,
its current
> version is able to
> > integrate with projects. In fact, I was
looking for
> projects like
> > ChemicalToolBoX because I would like to
develop my tools
> under project that
> > has more options. In this way, ChemicalToolBoX
is a great
> opportunity for
> > me.
> > Can you update the trello card with my
project? Is it
> necessary for your
> > organization?
>
> I added you :) So you have all right to modify
cards.
> Let me know if you need help with Tool
development or git.
>
> This is exciting!
> Cheers,
> Bjoern
>
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> 
>>
> > wrote:
> >
> >>
> >>
   

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi Bjorn, I've created the pull request [1] in your repository. I will be
grateful if you can assist me with the functional tests on the docking tool
and the final validation of the tool dependencies.

[1] https://github.com/bgruening/galaxytools/pull/310

Thanks a lot!

Best regards,

On Mon, Mar 14, 2016 at 12:56 PM Léo Biscassi 
wrote:

> Hi, thanks for the reply.
> About the branch model, ok! I'll follow the model presented.
> About the error in planemo functional tests, the problem is that the
> content of example output is not the same of output file of test. This is
> shown by the command diff performed on planemo test.
> Today, I'll create a pull request in your repository for that we can fix
> the problem.
> Thank for the helps.
>
> I'm excited about this.
>
> Best regards,
>
>
>
> On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
> wrote:
>
>>
>>
>> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
>> > Hi folks,
>> > I have make somes alterations on my tools to adjust of according with
>> > best pratices of development of tools presented in [1] [2]. The
>> > repository of tools was changed for [3].
>> > I was testing the tool of docking [4] with the command planemo t, but as
>> > the algorithm used is heuristic, the output files not have the same
>> > content that as output files example and planemo tests fails. Any
>> > suggestion to solve this problem?
>>
>> Is there anything in the file that is the same? Filesize? Some lines
>> that are everytime the same (no matter where in the file)?
>>
>> You could create a PR and I will review it and give you feedback.
>> Cheers,
>> Bjoern
>>
>>
>> > [1]
>> >
>> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
>> > [2] https://planemo.readthedocs.org/en/latest/
>> > [3] https://github.com/leobiscassi/autodock_vina_tools
>> > [4]
>> >
>> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
>> >
>> > Att.
>> >
>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi > > > wrote:
>> >
>> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
>> > in [1]? Could guide me about it?
>> >
>> > [1]
>> https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
>> >
>> > Att.
>> >
>> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi <
>> leo.bisca...@gmail.com
>> > > wrote:
>> >
>> > Ok, thanks!
>> >
>> > Best regards,
>> >
>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>> > >
>> > wrote:
>> >
>> >
>> >
>> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
>> > > Hi,
>> > > Thanks all your attention.
>> > > Although my project is functional prototype, its current
>> > version is able to
>> > > integrate with projects. In fact, I was looking for
>> > projects like
>> > > ChemicalToolBoX because I would like to develop my tools
>> > under project that
>> > > has more options. In this way, ChemicalToolBoX is a great
>> > opportunity for
>> > > me.
>> > > Can you update the trello card with my project? Is it
>> > necessary for your
>> > > organization?
>> >
>> > I added you :) So you have all right to modify cards.
>> > Let me know if you need help with Tool development or git.
>> >
>> > This is exciting!
>> > Cheers,
>> > Bjoern
>> >
>> > > Best regards,
>> > >
>> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
>> >  bjoern.gruen...@gmail.com>>
>> > > wrote:
>> > >
>> > >>
>> > >>
>> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>> > >>> Hi,
>> > >>>
>> > >>> I've found this Trello card (
>> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration).
>> > Do you have more
>> > >>> information about it?
>> > >>
>> > >> Afaik we can not use his work as it was done for some
>> > company and he
>> > >> moved on ... so this is unfortunately no option afaik.
>> > >>
>> > >>
>> > >>
>> > >>> best,
>> > >>>
>> > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
>> >  bjoern.gruen...@gmail.com>
>> > >>>
>> > >>> wrote:
>> > >>>
>> >  Hi,
>> > 
>> >  yes we had some idea, but nothing materialised so far.
>> > We started with
>> >  the visualisation, 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi, thanks for the reply.
About the branch model, ok! I'll follow the model presented.
About the error in planemo functional tests, the problem is that the
content of example output is not the same of output file of test. This is
shown by the command diff performed on planemo test.
Today, I'll create a pull request in your repository for that we can fix
the problem.
Thank for the helps.

I'm excited about this.

Best regards,



On Thu, Mar 10, 2016 at 5:51 PM Björn Grüning 
wrote:

>
>
> Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> > Hi folks,
> > I have make somes alterations on my tools to adjust of according with
> > best pratices of development of tools presented in [1] [2]. The
> > repository of tools was changed for [3].
> > I was testing the tool of docking [4] with the command planemo t, but as
> > the algorithm used is heuristic, the output files not have the same
> > content that as output files example and planemo tests fails. Any
> > suggestion to solve this problem?
>
> Is there anything in the file that is the same? Filesize? Some lines
> that are everytime the same (no matter where in the file)?
>
> You could create a PR and I will review it and give you feedback.
> Cheers,
> Bjoern
>
>
> > [1]
> >
> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> > [2] https://planemo.readthedocs.org/en/latest/
> > [3] https://github.com/leobiscassi/autodock_vina_tools
> > [4]
> >
> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
> >
> > Att.
> >
> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi  > > wrote:
> >
> > Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
> > in [1]? Could guide me about it?
> >
> > [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi  > > wrote:
> >
> > Ok, thanks!
> >
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> > >
> > wrote:
> >
> >
> >
> > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > > Hi,
> > > Thanks all your attention.
> > > Although my project is functional prototype, its current
> > version is able to
> > > integrate with projects. In fact, I was looking for
> > projects like
> > > ChemicalToolBoX because I would like to develop my tools
> > under project that
> > > has more options. In this way, ChemicalToolBoX is a great
> > opportunity for
> > > me.
> > > Can you update the trello card with my project? Is it
> > necessary for your
> > > organization?
> >
> > I added you :) So you have all right to modify cards.
> > Let me know if you need help with Tool development or git.
> >
> > This is exciting!
> > Cheers,
> > Bjoern
> >
> > > Best regards,
> > >
> > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> >  >>
> > > wrote:
> > >
> > >>
> > >>
> > >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> > >>> Hi,
> > >>>
> > >>> I've found this Trello card (
> > >>> https://trello.com/c/2eIu6SBa/49-autodock-integration).
> > Do you have more
> > >>> information about it?
> > >>
> > >> Afaik we can not use his work as it was done for some
> > company and he
> > >> moved on ... so this is unfortunately no option afaik.
> > >>
> > >>
> > >>
> > >>> best,
> > >>>
> > >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
> >  >
> > >>>
> > >>> wrote:
> > >>>
> >  Hi,
> > 
> >  yes we had some idea, but nothing materialised so far.
> > We started with
> >  the visualisation, because this was more fun :)
> > 
> >  Have a look at this board for more ideas:
> >  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> > 
> >  Ciao,
> >  Bjoern
> > 
> > 
> >  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > > Hi Bjorn, thanks for reply.
> > > Would be great idea join forces in this project. How
> >

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Am 10.03.2016 um 21:30 schrieb Léo Biscassi:
> Hi folks,
> I have make somes alterations on my tools to adjust of according with
> best pratices of development of tools presented in [1] [2]. The
> repository of tools was changed for [3].
> I was testing the tool of docking [4] with the command planemo t, but as
> the algorithm used is heuristic, the output files not have the same
> content that as output files example and planemo tests fails. Any
> suggestion to solve this problem?

Is there anything in the file that is the same? Filesize? Some lines
that are everytime the same (no matter where in the file)?

You could create a PR and I will review it and give you feedback.
Cheers,
Bjoern


> [1]
> https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html
> [2] https://planemo.readthedocs.org/en/latest/
> [3] https://github.com/leobiscassi/autodock_vina_tools
> [4]
> https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/docking
> 
> Att.
> 
> On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi  > wrote:
> 
> Hi Bjorn, the branch model of ChemicalToolBoX is the same presented
> in [1]? Could guide me about it?
> 
> [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
> 
> Att.
> 
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi  > wrote:
> 
> Ok, thanks!
> 
> Best regards,
> 
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> >
> wrote:
> 
> 
> 
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional prototype, its current
> version is able to
> > integrate with projects. In fact, I was looking for
> projects like
> > ChemicalToolBoX because I would like to develop my tools
> under project that
> > has more options. In this way, ChemicalToolBoX is a great
> opportunity for
> > me.
> > Can you update the trello card with my project? Is it
> necessary for your
> > organization?
> 
> I added you :) So you have all right to modify cards.
> Let me know if you need help with Tool development or git.
> 
> This is exciting!
> Cheers,
> Bjoern
> 
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> >
> > wrote:
> >
> >>
> >>
> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> >>> Hi,
> >>>
> >>> I've found this Trello card (
> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration).
> Do you have more
> >>> information about it?
> >>
> >> Afaik we can not use his work as it was done for some
> company and he
> >> moved on ... so this is unfortunately no option afaik.
> >>
> >>
> >>
> >>> best,
> >>>
> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
> 
> >>>
> >>> wrote:
> >>>
>  Hi,
> 
>  yes we had some idea, but nothing materialised so far.
> We started with
>  the visualisation, because this was more fun :)
> 
>  Have a look at this board for more ideas:
>  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> 
>  Ciao,
>  Bjoern
> 
> 
>  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > Hi Bjorn, thanks for reply.
> > Would be great idea join forces in this project. How
> do you plan extend
> > ChemicalToolBoX with docking? I would like to know
> more details.
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
> >> bjoern.gruen...@gmail.com 
> >
> > wrote:
> >
> >> Hi Léo,
> >>
> >> idneed we have a small community that is bringing
> Cheminformatics into
> >> the Galaxy. It's called ChemicalToolBox and is
> located here:
> >>
> >>
> 
> 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Hi,

yes it more or less the same.

1) You fork the galaxytools repository in github.
2) You clone your fork of galaxtools
3) now inside of your clone you do:
 - git branch autodock
 - git checkout autodock
4) add your tools and modfiy any file you want with
 - git add ./foo/bar
 - git commit -m 'add awesome autodock tools'
5) push your changes to your fork with
 - git push origin autodock <- this is your branch name
6) go to github and create a PR against my galaxytools repository

Oh this exciting!
Thanks!
Bjoern

Am 30.01.2016 um 19:44 schrieb Léo Biscassi:
> Hi Bjorn, the branch model of ChemicalToolBoX is the same presented in
> [1]? Could guide me about it?
> 
> [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md
> 
> Att.
> 
> On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi  > wrote:
> 
> Ok, thanks!
> 
> Best regards,
> 
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
> > wrote:
> 
> 
> 
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional prototype, its current
> version is able to
> > integrate with projects. In fact, I was looking for projects like
> > ChemicalToolBoX because I would like to develop my tools under
> project that
> > has more options. In this way, ChemicalToolBoX is a great
> opportunity for
> > me.
> > Can you update the trello card with my project? Is it
> necessary for your
> > organization?
> 
> I added you :) So you have all right to modify cards.
> Let me know if you need help with Tool development or git.
> 
> This is exciting!
> Cheers,
> Bjoern
> 
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning
> >
> > wrote:
> >
> >>
> >>
> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> >>> Hi,
> >>>
> >>> I've found this Trello card (
> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do
> you have more
> >>> information about it?
> >>
> >> Afaik we can not use his work as it was done for some company
> and he
> >> moved on ... so this is unfortunately no option afaik.
> >>
> >>
> >>
> >>> best,
> >>>
> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning
> 
> >>>
> >>> wrote:
> >>>
>  Hi,
> 
>  yes we had some idea, but nothing materialised so far. We
> started with
>  the visualisation, because this was more fun :)
> 
>  Have a look at this board for more ideas:
>  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> 
>  Ciao,
>  Bjoern
> 
> 
>  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > Hi Bjorn, thanks for reply.
> > Would be great idea join forces in this project. How do
> you plan extend
> > ChemicalToolBoX with docking? I would like to know more
> details.
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
> >> bjoern.gruen...@gmail.com 
> >
> > wrote:
> >
> >> Hi Léo,
> >>
> >> idneed we have a small community that is bringing
> Cheminformatics into
> >> the Galaxy. It's called ChemicalToolBox and is located here:
> >>
> >>
> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
> >>
> >> We have all the basic stuff for manipulating checmical
> structure
> >> files,
> >> fingerprint search, pharmacophore searches and so on.
> Also we did all
> >> the basic work on datatypes and packages. Our last
> addition was to
> >> integrate a PDB visulalisation (NGL) based on WebGL. This
> one is used
> >> to
> >> visualise our structures directly in Galaxy.
> >>
> >> We have also a trello board with more ideas and plans
> what we would
> >> like
> >> to add and Vina is one of the ig targets :)
> >> Would be great if we can join forces here!
> >>
> >> We also maintain a Galaxy Flavour (Galaxy Docker Image about
> >> Cheminformatics) that we would love to extend with 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi Bjorn, the branch model of ChemicalToolBoX is the same presented in [1]?
Could guide me about it?

[1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md

Att.

On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi  wrote:

> Ok, thanks!
>
> Best regards,
>
> On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning 
> wrote:
>
>>
>>
>> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
>> > Hi,
>> > Thanks all your attention.
>> > Although my project is functional prototype, its current version is
>> able to
>> > integrate with projects. In fact, I was looking for projects like
>> > ChemicalToolBoX because I would like to develop my tools under project
>> that
>> > has more options. In this way, ChemicalToolBoX is a great opportunity
>> for
>> > me.
>> > Can you update the trello card with my project? Is it necessary for your
>> > organization?
>>
>> I added you :) So you have all right to modify cards.
>> Let me know if you need help with Tool development or git.
>>
>> This is exciting!
>> Cheers,
>> Bjoern
>>
>> > Best regards,
>> >
>> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning <
>> bjoern.gruen...@gmail.com>
>> > wrote:
>> >
>> >>
>> >>
>> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>> >>> Hi,
>> >>>
>> >>> I've found this Trello card (
>> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have
>> more
>> >>> information about it?
>> >>
>> >> Afaik we can not use his work as it was done for some company and he
>> >> moved on ... so this is unfortunately no option afaik.
>> >>
>> >>
>> >>
>> >>> best,
>> >>>
>> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning <
>> bjoern.gruen...@gmail.com
>> >>>
>> >>> wrote:
>> >>>
>>  Hi,
>> 
>>  yes we had some idea, but nothing materialised so far. We started
>> with
>>  the visualisation, because this was more fun :)
>> 
>>  Have a look at this board for more ideas:
>>  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
>> 
>>  Ciao,
>>  Bjoern
>> 
>> 
>>  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
>> > Hi Bjorn, thanks for reply.
>> > Would be great idea join forces in this project. How do you plan
>> extend
>> > ChemicalToolBoX with docking? I would like to know more details.
>> >
>> > Att.
>> >
>> > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
>> >> bjoern.gruen...@gmail.com
>> >
>> > wrote:
>> >
>> >> Hi Léo,
>> >>
>> >> idneed we have a small community that is bringing Cheminformatics
>> into
>> >> the Galaxy. It's called ChemicalToolBox and is located here:
>> >>
>> >>
>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
>> >>
>> >> We have all the basic stuff for manipulating checmical structure
>> >> files,
>> >> fingerprint search, pharmacophore searches and so on. Also we did
>> all
>> >> the basic work on datatypes and packages. Our last addition was to
>> >> integrate a PDB visulalisation (NGL) based on WebGL. This one is
>> used
>> >> to
>> >> visualise our structures directly in Galaxy.
>> >>
>> >> We have also a trello board with more ideas and plans what we would
>> >> like
>> >> to add and Vina is one of the ig targets :)
>> >> Would be great if we can join forces here!
>> >>
>> >> We also maintain a Galaxy Flavour (Galaxy Docker Image about
>> >> Cheminformatics) that we would love to extend with Docking.
>> >>
>> >> Thanks for letting us know and looking forward to join forces here!
>> >> Bjoern
>> >>
>> >>
>> >> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
>> >>> Hi folks,
>> >>>
>> >>> I've been developing Galaxy tools for docking protein-compounds.
>> My
>> >> docking
>> >>> program is Autodock Vina. In [1] is my repository.
>> >>>
>> >>> I'm writing here for two purpose:
>> >>> 1) Is there someone working in this way? I've found the project
>> [2].
>> >>> 2) I would like to share these tools to Galaxy project. Are they
>>  welcome
>> >>> for Galaxy project?  Let me know the best practices for developing
>>  tools
>> >> to
>> >>> be shared in Galaxy project.
>> >>>
>> >>> [1] https://github.com/leobiscassi/galaxy_tools
>> >>> [2] https://toolshed.g2.bx.psu.edu/
>> >>>
>> >>> Thanks for any help.
>> >>>
>> >>> Att.
>> >>>
>> >>>
>> >>>
>> >>> ___
>> >>> 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/
>> >>>
>> >>
>> 
>> >>
>>
> --
> *Léo Biscassi*
> Facebook - 

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Hi Léo,

idneed we have a small community that is bringing Cheminformatics into
the Galaxy. It's called ChemicalToolBox and is located here:

https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox

We have all the basic stuff for manipulating checmical structure files,
fingerprint search, pharmacophore searches and so on. Also we did all
the basic work on datatypes and packages. Our last addition was to
integrate a PDB visulalisation (NGL) based on WebGL. This one is used to
visualise our structures directly in Galaxy.

We have also a trello board with more ideas and plans what we would like
to add and Vina is one of the ig targets :)
Would be great if we can join forces here!

We also maintain a Galaxy Flavour (Galaxy Docker Image about
Cheminformatics) that we would love to extend with Docking.

Thanks for letting us know and looking forward to join forces here!
Bjoern


Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> Hi folks,
> 
> I've been developing Galaxy tools for docking protein-compounds. My docking
> program is Autodock Vina. In [1] is my repository.
> 
> I'm writing here for two purpose:
> 1) Is there someone working in this way? I've found the project [2].
> 2) I would like to share these tools to Galaxy project. Are they welcome
> for Galaxy project?  Let me know the best practices for developing tools to
> be shared in Galaxy project.
> 
> [1] https://github.com/leobiscassi/galaxy_tools
> [2] https://toolshed.g2.bx.psu.edu/
> 
> Thanks for any help.
> 
> Att.
> 
> 
> 
> ___
> 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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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Martin Čech]

Hello Léo,

all tool are sincerely welcomed in the Galaxy Tool Shed.

Good tutorial for tool writing is a part of Planemo documentation:
https://planemo.readthedocs.org/en/latest/writing.html
Planemo is a command line toolset aimed at helping tool developers like you
getting their tools into Galaxy and the Tool Shed.
Also have a look at https://github.com/galaxyproject/tools-iuc for tool
writing inspiration and
http://galaxy-iuc-standards.readthedocs.org/en/latest/ for best practices.

Let us know if we can help.

Thank you for using Galaxy.

M.

On Mon, Dec 28, 2015 at 12:58 PM Léo Biscassi 
wrote:

> Hi folks,
>
> I've been developing Galaxy tools for docking protein-compounds. My
> docking program is Autodock Vina. In [1] is my repository.
>
> I'm writing here for two purpose:
> 1) Is there someone working in this way? I've found the project [2].
> 2) I would like to share these tools to Galaxy project. Are they welcome
> for Galaxy project?  Let me know the best practices for developing tools to
> be shared in Galaxy project.
>
> [1] https://github.com/leobiscassi/galaxy_tools
> [2] https://toolshed.g2.bx.psu.edu/
>
> Thanks for any help.
>
> Att.
> --
> *Léo Biscassi*
> Facebook - https://pt-br.facebook.com/lbiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
> Twitter - https://twitter.com/leobiscassi
> ___
> 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/

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi Martin,
I'll take a look at the tutorials, thanks!

Att.

On Mon, Dec 28, 2015 at 4:10 PM Martin Čech  wrote:

> Hello Léo,
>
> all tool are sincerely welcomed in the Galaxy Tool Shed.
>
> Good tutorial for tool writing is a part of Planemo documentation:
> https://planemo.readthedocs.org/en/latest/writing.html
> Planemo is a command line toolset aimed at helping tool developers like
> you getting their tools into Galaxy and the Tool Shed.
> Also have a look at https://github.com/galaxyproject/tools-iuc for tool
> writing inspiration and
> http://galaxy-iuc-standards.readthedocs.org/en/latest/ for best practices.
>
> Let us know if we can help.
>
> Thank you for using Galaxy.
>
> M.
>
> On Mon, Dec 28, 2015 at 12:58 PM Léo Biscassi 
> wrote:
>
>> Hi folks,
>>
>> I've been developing Galaxy tools for docking protein-compounds. My
>> docking program is Autodock Vina. In [1] is my repository.
>>
>> I'm writing here for two purpose:
>> 1) Is there someone working in this way? I've found the project [2].
>> 2) I would like to share these tools to Galaxy project. Are they welcome
>> for Galaxy project?  Let me know the best practices for developing tools to
>> be shared in Galaxy project.
>>
>> [1] https://github.com/leobiscassi/galaxy_tools
>> [2] https://toolshed.g2.bx.psu.edu/
>>
>> Thanks for any help.
>>
>> Att.
>> --
>> *Léo Biscassi*
>> Facebook - https://pt-br.facebook.com/lbiscassi
>> Linkedin - https://br.linkedin.com/in/leobiscassi
>> Skype - biscassi.leo
>> Twitter - https://twitter.com/leobiscassi
>>
> ___
>> 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/
>
> --
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
___
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi Bjorn, thanks for reply.
Would be great idea join forces in this project. How do you plan extend
ChemicalToolBoX with docking? I would like to know more details.

Att.

On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning 
wrote:

> Hi Léo,
>
> idneed we have a small community that is bringing Cheminformatics into
> the Galaxy. It's called ChemicalToolBox and is located here:
>
> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
>
> We have all the basic stuff for manipulating checmical structure files,
> fingerprint search, pharmacophore searches and so on. Also we did all
> the basic work on datatypes and packages. Our last addition was to
> integrate a PDB visulalisation (NGL) based on WebGL. This one is used to
> visualise our structures directly in Galaxy.
>
> We have also a trello board with more ideas and plans what we would like
> to add and Vina is one of the ig targets :)
> Would be great if we can join forces here!
>
> We also maintain a Galaxy Flavour (Galaxy Docker Image about
> Cheminformatics) that we would love to extend with Docking.
>
> Thanks for letting us know and looking forward to join forces here!
> Bjoern
>
>
> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> > Hi folks,
> >
> > I've been developing Galaxy tools for docking protein-compounds. My
> docking
> > program is Autodock Vina. In [1] is my repository.
> >
> > I'm writing here for two purpose:
> > 1) Is there someone working in this way? I've found the project [2].
> > 2) I would like to share these tools to Galaxy project. Are they welcome
> > for Galaxy project?  Let me know the best practices for developing tools
> to
> > be shared in Galaxy project.
> >
> > [1] https://github.com/leobiscassi/galaxy_tools
> > [2] https://toolshed.g2.bx.psu.edu/
> >
> > Thanks for any help.
> >
> > Att.
> >
> >
> >
> > ___
> > 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/
> >
>
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi,

I've found this Trello card (
https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more
information about it?

best,

On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning 
wrote:

> Hi,
>
> yes we had some idea, but nothing materialised so far. We started with
> the visualisation, because this was more fun :)
>
> Have a look at this board for more ideas:
> https://trello.com/b/t9Wr8lSY/chemicaltoolbox
>
> Ciao,
> Bjoern
>
>
> Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > Hi Bjorn, thanks for reply.
> > Would be great idea join forces in this project. How do you plan extend
> > ChemicalToolBoX with docking? I would like to know more details.
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning  >
> > wrote:
> >
> >> Hi Léo,
> >>
> >> idneed we have a small community that is bringing Cheminformatics into
> >> the Galaxy. It's called ChemicalToolBox and is located here:
> >>
> >> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
> >>
> >> We have all the basic stuff for manipulating checmical structure files,
> >> fingerprint search, pharmacophore searches and so on. Also we did all
> >> the basic work on datatypes and packages. Our last addition was to
> >> integrate a PDB visulalisation (NGL) based on WebGL. This one is used to
> >> visualise our structures directly in Galaxy.
> >>
> >> We have also a trello board with more ideas and plans what we would like
> >> to add and Vina is one of the ig targets :)
> >> Would be great if we can join forces here!
> >>
> >> We also maintain a Galaxy Flavour (Galaxy Docker Image about
> >> Cheminformatics) that we would love to extend with Docking.
> >>
> >> Thanks for letting us know and looking forward to join forces here!
> >> Bjoern
> >>
> >>
> >> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> >>> Hi folks,
> >>>
> >>> I've been developing Galaxy tools for docking protein-compounds. My
> >> docking
> >>> program is Autodock Vina. In [1] is my repository.
> >>>
> >>> I'm writing here for two purpose:
> >>> 1) Is there someone working in this way? I've found the project [2].
> >>> 2) I would like to share these tools to Galaxy project. Are they
> welcome
> >>> for Galaxy project?  Let me know the best practices for developing
> tools
> >> to
> >>> be shared in Galaxy project.
> >>>
> >>> [1] https://github.com/leobiscassi/galaxy_tools
> >>> [2] https://toolshed.g2.bx.psu.edu/
> >>>
> >>> Thanks for any help.
> >>>
> >>> Att.
> >>>
> >>>
> >>>
> >>> ___
> >>> 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/
> >>>
> >>
>
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
___
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/

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Ok, thanks!

Best regards,

On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning 
wrote:

>
>
> Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> > Hi,
> > Thanks all your attention.
> > Although my project is functional prototype, its current version is able
> to
> > integrate with projects. In fact, I was looking for projects like
> > ChemicalToolBoX because I would like to develop my tools under project
> that
> > has more options. In this way, ChemicalToolBoX is a great opportunity for
> > me.
> > Can you update the trello card with my project? Is it necessary for your
> > organization?
>
> I added you :) So you have all right to modify cards.
> Let me know if you need help with Tool development or git.
>
> This is exciting!
> Cheers,
> Bjoern
>
> > Best regards,
> >
> > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning  >
> > wrote:
> >
> >>
> >>
> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> >>> Hi,
> >>>
> >>> I've found this Trello card (
> >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have
> more
> >>> information about it?
> >>
> >> Afaik we can not use his work as it was done for some company and he
> >> moved on ... so this is unfortunately no option afaik.
> >>
> >>
> >>
> >>> best,
> >>>
> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning <
> bjoern.gruen...@gmail.com
> >>>
> >>> wrote:
> >>>
>  Hi,
> 
>  yes we had some idea, but nothing materialised so far. We started with
>  the visualisation, because this was more fun :)
> 
>  Have a look at this board for more ideas:
>  https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> 
>  Ciao,
>  Bjoern
> 
> 
>  Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> > Hi Bjorn, thanks for reply.
> > Would be great idea join forces in this project. How do you plan
> extend
> > ChemicalToolBoX with docking? I would like to know more details.
> >
> > Att.
> >
> > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
> >> bjoern.gruen...@gmail.com
> >
> > wrote:
> >
> >> Hi Léo,
> >>
> >> idneed we have a small community that is bringing Cheminformatics
> into
> >> the Galaxy. It's called ChemicalToolBox and is located here:
> >>
> >>
> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
> >>
> >> We have all the basic stuff for manipulating checmical structure
> >> files,
> >> fingerprint search, pharmacophore searches and so on. Also we did
> all
> >> the basic work on datatypes and packages. Our last addition was to
> >> integrate a PDB visulalisation (NGL) based on WebGL. This one is
> used
> >> to
> >> visualise our structures directly in Galaxy.
> >>
> >> We have also a trello board with more ideas and plans what we would
> >> like
> >> to add and Vina is one of the ig targets :)
> >> Would be great if we can join forces here!
> >>
> >> We also maintain a Galaxy Flavour (Galaxy Docker Image about
> >> Cheminformatics) that we would love to extend with Docking.
> >>
> >> Thanks for letting us know and looking forward to join forces here!
> >> Bjoern
> >>
> >>
> >> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> >>> Hi folks,
> >>>
> >>> I've been developing Galaxy tools for docking protein-compounds. My
> >> docking
> >>> program is Autodock Vina. In [1] is my repository.
> >>>
> >>> I'm writing here for two purpose:
> >>> 1) Is there someone working in this way? I've found the project
> [2].
> >>> 2) I would like to share these tools to Galaxy project. Are they
>  welcome
> >>> for Galaxy project?  Let me know the best practices for developing
>  tools
> >> to
> >>> be shared in Galaxy project.
> >>>
> >>> [1] https://github.com/leobiscassi/galaxy_tools
> >>> [2] https://toolshed.g2.bx.psu.edu/
> >>>
> >>> Thanks for any help.
> >>>
> >>> Att.
> >>>
> >>>
> >>>
> >>> ___
> >>> 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/
> >>>
> >>
> 
> >>
>
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
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Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> Hi,
> 
> I've found this Trello card (
> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more
> information about it?

Afaik we can not use his work as it was done for some company and he
moved on ... so this is unfortunately no option afaik.



> best,
> 
> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning 
> wrote:
> 
>> Hi,
>>
>> yes we had some idea, but nothing materialised so far. We started with
>> the visualisation, because this was more fun :)
>>
>> Have a look at this board for more ideas:
>> https://trello.com/b/t9Wr8lSY/chemicaltoolbox
>>
>> Ciao,
>> Bjoern
>>
>>
>> Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
>>> Hi Bjorn, thanks for reply.
>>> Would be great idea join forces in this project. How do you plan extend
>>> ChemicalToolBoX with docking? I would like to know more details.
>>>
>>> Att.
>>>
>>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning >>
>>> wrote:
>>>
 Hi Léo,

 idneed we have a small community that is bringing Cheminformatics into
 the Galaxy. It's called ChemicalToolBox and is located here:

 https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox

 We have all the basic stuff for manipulating checmical structure files,
 fingerprint search, pharmacophore searches and so on. Also we did all
 the basic work on datatypes and packages. Our last addition was to
 integrate a PDB visulalisation (NGL) based on WebGL. This one is used to
 visualise our structures directly in Galaxy.

 We have also a trello board with more ideas and plans what we would like
 to add and Vina is one of the ig targets :)
 Would be great if we can join forces here!

 We also maintain a Galaxy Flavour (Galaxy Docker Image about
 Cheminformatics) that we would love to extend with Docking.

 Thanks for letting us know and looking forward to join forces here!
 Bjoern


 Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> Hi folks,
>
> I've been developing Galaxy tools for docking protein-compounds. My
 docking
> program is Autodock Vina. In [1] is my repository.
>
> I'm writing here for two purpose:
> 1) Is there someone working in this way? I've found the project [2].
> 2) I would like to share these tools to Galaxy project. Are they
>> welcome
> for Galaxy project?  Let me know the best practices for developing
>> tools
 to
> be shared in Galaxy project.
>
> [1] https://github.com/leobiscassi/galaxy_tools
> [2] https://toolshed.g2.bx.psu.edu/
>
> Thanks for any help.
>
> Att.
>
>
>
> ___
> 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] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Am 28.12.2015 um 20:33 schrieb Léo Biscassi:
> Hi,
> Thanks all your attention.
> Although my project is functional prototype, its current version is able to
> integrate with projects. In fact, I was looking for projects like
> ChemicalToolBoX because I would like to develop my tools under project that
> has more options. In this way, ChemicalToolBoX is a great opportunity for
> me.
> Can you update the trello card with my project? Is it necessary for your
> organization?

I added you :) So you have all right to modify cards.
Let me know if you need help with Tool development or git.

This is exciting!
Cheers,
Bjoern

> Best regards,
> 
> On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning 
> wrote:
> 
>>
>>
>> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
>>> Hi,
>>>
>>> I've found this Trello card (
>>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more
>>> information about it?
>>
>> Afaik we can not use his work as it was done for some company and he
>> moved on ... so this is unfortunately no option afaik.
>>
>>
>>
>>> best,
>>>
>>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning >>
>>> wrote:
>>>
 Hi,

 yes we had some idea, but nothing materialised so far. We started with
 the visualisation, because this was more fun :)

 Have a look at this board for more ideas:
 https://trello.com/b/t9Wr8lSY/chemicaltoolbox

 Ciao,
 Bjoern


 Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> Hi Bjorn, thanks for reply.
> Would be great idea join forces in this project. How do you plan extend
> ChemicalToolBoX with docking? I would like to know more details.
>
> Att.
>
> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
>> bjoern.gruen...@gmail.com
>
> wrote:
>
>> Hi Léo,
>>
>> idneed we have a small community that is bringing Cheminformatics into
>> the Galaxy. It's called ChemicalToolBox and is located here:
>>
>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
>>
>> We have all the basic stuff for manipulating checmical structure
>> files,
>> fingerprint search, pharmacophore searches and so on. Also we did all
>> the basic work on datatypes and packages. Our last addition was to
>> integrate a PDB visulalisation (NGL) based on WebGL. This one is used
>> to
>> visualise our structures directly in Galaxy.
>>
>> We have also a trello board with more ideas and plans what we would
>> like
>> to add and Vina is one of the ig targets :)
>> Would be great if we can join forces here!
>>
>> We also maintain a Galaxy Flavour (Galaxy Docker Image about
>> Cheminformatics) that we would love to extend with Docking.
>>
>> Thanks for letting us know and looking forward to join forces here!
>> Bjoern
>>
>>
>> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
>>> Hi folks,
>>>
>>> I've been developing Galaxy tools for docking protein-compounds. My
>> docking
>>> program is Autodock Vina. In [1] is my repository.
>>>
>>> I'm writing here for two purpose:
>>> 1) Is there someone working in this way? I've found the project [2].
>>> 2) I would like to share these tools to Galaxy project. Are they
 welcome
>>> for Galaxy project?  Let me know the best practices for developing
 tools
>> to
>>> be shared in Galaxy project.
>>>
>>> [1] https://github.com/leobiscassi/galaxy_tools
>>> [2] https://toolshed.g2.bx.psu.edu/
>>>
>>> Thanks for any help.
>>>
>>> Att.
>>>
>>>
>>>
>>> ___
>>> 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] Galaxy tools for docking protein-compounds.

[Björn Grüning]

Hi,

yes we had some idea, but nothing materialised so far. We started with
the visualisation, because this was more fun :)

Have a look at this board for more ideas:
https://trello.com/b/t9Wr8lSY/chemicaltoolbox

Ciao,
Bjoern


Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> Hi Bjorn, thanks for reply.
> Would be great idea join forces in this project. How do you plan extend
> ChemicalToolBoX with docking? I would like to know more details.
> 
> Att.
> 
> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning 
> wrote:
> 
>> Hi Léo,
>>
>> idneed we have a small community that is bringing Cheminformatics into
>> the Galaxy. It's called ChemicalToolBox and is located here:
>>
>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
>>
>> We have all the basic stuff for manipulating checmical structure files,
>> fingerprint search, pharmacophore searches and so on. Also we did all
>> the basic work on datatypes and packages. Our last addition was to
>> integrate a PDB visulalisation (NGL) based on WebGL. This one is used to
>> visualise our structures directly in Galaxy.
>>
>> We have also a trello board with more ideas and plans what we would like
>> to add and Vina is one of the ig targets :)
>> Would be great if we can join forces here!
>>
>> We also maintain a Galaxy Flavour (Galaxy Docker Image about
>> Cheminformatics) that we would love to extend with Docking.
>>
>> Thanks for letting us know and looking forward to join forces here!
>> Bjoern
>>
>>
>> Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
>>> Hi folks,
>>>
>>> I've been developing Galaxy tools for docking protein-compounds. My
>> docking
>>> program is Autodock Vina. In [1] is my repository.
>>>
>>> I'm writing here for two purpose:
>>> 1) Is there someone working in this way? I've found the project [2].
>>> 2) I would like to share these tools to Galaxy project. Are they welcome
>>> for Galaxy project?  Let me know the best practices for developing tools
>> to
>>> be shared in Galaxy project.
>>>
>>> [1] https://github.com/leobiscassi/galaxy_tools
>>> [2] https://toolshed.g2.bx.psu.edu/
>>>
>>> Thanks for any help.
>>>
>>> Att.
>>>
>>>
>>>
>>> ___
>>> 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] Galaxy tools for docking protein-compounds.

[Léo Biscassi]

Hi,
Thanks all your attention.
Although my project is functional prototype, its current version is able to
integrate with projects. In fact, I was looking for projects like
ChemicalToolBoX because I would like to develop my tools under project that
has more options. In this way, ChemicalToolBoX is a great opportunity for
me.
Can you update the trello card with my project? Is it necessary for your
organization?

Best regards,

On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning 
wrote:

>
>
> Am 28.12.2015 um 20:06 schrieb Léo Biscassi:
> > Hi,
> >
> > I've found this Trello card (
> > https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more
> > information about it?
>
> Afaik we can not use his work as it was done for some company and he
> moved on ... so this is unfortunately no option afaik.
>
>
>
> > best,
> >
> > On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning  >
> > wrote:
> >
> >> Hi,
> >>
> >> yes we had some idea, but nothing materialised so far. We started with
> >> the visualisation, because this was more fun :)
> >>
> >> Have a look at this board for more ideas:
> >> https://trello.com/b/t9Wr8lSY/chemicaltoolbox
> >>
> >> Ciao,
> >> Bjoern
> >>
> >>
> >> Am 28.12.2015 um 19:29 schrieb Léo Biscassi:
> >>> Hi Bjorn, thanks for reply.
> >>> Would be great idea join forces in this project. How do you plan extend
> >>> ChemicalToolBoX with docking? I would like to know more details.
> >>>
> >>> Att.
> >>>
> >>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <
> bjoern.gruen...@gmail.com
> >>>
> >>> wrote:
> >>>
>  Hi Léo,
> 
>  idneed we have a small community that is bringing Cheminformatics into
>  the Galaxy. It's called ChemicalToolBox and is located here:
> 
>  https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox
> 
>  We have all the basic stuff for manipulating checmical structure
> files,
>  fingerprint search, pharmacophore searches and so on. Also we did all
>  the basic work on datatypes and packages. Our last addition was to
>  integrate a PDB visulalisation (NGL) based on WebGL. This one is used
> to
>  visualise our structures directly in Galaxy.
> 
>  We have also a trello board with more ideas and plans what we would
> like
>  to add and Vina is one of the ig targets :)
>  Would be great if we can join forces here!
> 
>  We also maintain a Galaxy Flavour (Galaxy Docker Image about
>  Cheminformatics) that we would love to extend with Docking.
> 
>  Thanks for letting us know and looking forward to join forces here!
>  Bjoern
> 
> 
>  Am 28.12.2015 um 18:58 schrieb Léo Biscassi:
> > Hi folks,
> >
> > I've been developing Galaxy tools for docking protein-compounds. My
>  docking
> > program is Autodock Vina. In [1] is my repository.
> >
> > I'm writing here for two purpose:
> > 1) Is there someone working in this way? I've found the project [2].
> > 2) I would like to share these tools to Galaxy project. Are they
> >> welcome
> > for Galaxy project?  Let me know the best practices for developing
> >> tools
>  to
> > be shared in Galaxy project.
> >
> > [1] https://github.com/leobiscassi/galaxy_tools
> > [2] https://toolshed.g2.bx.psu.edu/
> >
> > Thanks for any help.
> >
> > Att.
> >
> >
> >
> > ___
> > 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/
> >
> 
> >>
>
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
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