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 <mailto: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
<mailto: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>
> <mailto: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>
> <mailto: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>
<mailto: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>
<mailto: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>
<mailto: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>
<mailto: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
