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

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&gt; 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&gt; > 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&gt;&gt; >> > > 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&gt; >> > >>> >> > >>> 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&gt; >> > >>>>> >> > >>>>> 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 --