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

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