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 <bjoern.gruen...@gmail.com>
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 <leo.bisca...@gmail.com>
> 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 <bjoern.gruen...@gmail.com>
>> 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 <leo.bisca...@gmail.com
>>> > <mailto:leo.bisca...@gmail.com>> 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
>>> >     <mailto:leo.bisca...@gmail.com>> wrote:
>>> >
>>> >         Ok, thanks!
>>> >
>>> >         Best regards,
>>> >
>>> >         On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>>> >         <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>>
>>> >         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 <mailto:
>>> 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 <mailto:
>>> 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 <mailto:
>>> 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
>>> >
>>> >     --
>>> >     *Léo Biscassi*
>>> >     Facebook - https://pt-br.facebook.com/lbiscassi
>>> >     Linkedin - https://br.linkedin.com/in/leobiscassi
>>> >     Skype - biscassi.leo
>>> >     Twitter - https://twitter.com/leobiscassi
>>> >
>>> > --
>>> > *Léo Biscassi*
>>> > Facebook - https://pt-br.facebook.com/lbiscassi
>>> > Linkedin - https://br.linkedin.com/in/leobiscassi
>>> > Skype - biscassi.leo
>>> > Twitter - https://twitter.com/leobiscassi
>>>
>> --
>> *Léo Biscassi*
>> Universidade Estadual Santa Cruz - UESC
>> Mestrando em Modelagem Computacional
>> Lattes - http://lattes.cnpq.br/8274409384297485
>> Twitter - https://twitter.com/leobiscassi
>> Linkedin - https://br.linkedin.com/in/leobiscassi
>> Skype - biscassi.leo
>>
> --
> *Léo Biscassi*
> Universidade Estadual Santa Cruz - UESC
> Mestrando em Modelagem Computacional
> Lattes - http://lattes.cnpq.br/8274409384297485
> Twitter - https://twitter.com/leobiscassi
> Linkedin - https://br.linkedin.com/in/leobiscassi
> Skype - biscassi.leo
>
>
> --
*Léo Biscassi*
Universidade Estadual Santa Cruz - UESC
Mestrando em Modelagem Computacional
Lattes - http://lattes.cnpq.br/8274409384297485
Twitter - https://twitter.com/leobiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
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