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
<bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@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 <mailto:leo.biscassi@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
> <mailto:bjoern.gruening@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>
> > <mailto:leo.biscassi@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>
> > <mailto:leo.biscassi@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>
> <mailto:bjoern.gruening@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@gmail.com>
> <mailto:bjoern.gruening@gmail.com
> <mailto:bjoern.gruening@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@gmail.com>
> <mailto:bjoern.gruening@gmail.com
> <mailto:bjoern.gruening@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@gmail.com>
> <mailto:bjoern.gruening@gmail.com
> <mailto:bjoern.gruening@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