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.gruening(a)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.biscassi(a)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.gruening(a)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/doc...
>> >
>> > Att.
>> >
>> > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <leo.biscassi(a)gmail.com
>> > <mailto:leo.biscassi@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.biscassi(a)gmail.com
>> > <mailto:leo.biscassi@gmail.com>> wrote:
>> >
>> > Ok, thanks!
>> >
>> > Best regards,
>> >
>> > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning
>> > <bjoern.gruening(a)gmail.com
<mailto:bjoern.gruening@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.gruening(a)gmail.com <mailto:
>> bjoern.gruening(a)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.gruening(a)gmail.com <mailto:
>> bjoern.gruening(a)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.gruening(a)gmail.com <mailto:
>> bjoern.gruening(a)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 -