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

On 15.03.2016 18:11, Léo Biscassi wrote: 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

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

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 wrote: > Saw it! Will review it

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

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

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

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

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

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

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

Hi, yes it more or less the same. 1) You fork the galaxytools repository in github. 2) You clone your fork of galaxtools 3) now inside of your clone you do: - git branch autodock - git checkout autodock 4) add your tools and modfiy any file you want with - git add ./foo/bar - git commit -m

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

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 wrote: > Ok, thanks! > > Best regards, > > On

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

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

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

Hello Léo, all tool are sincerely welcomed in the Galaxy Tool Shed. Good tutorial for tool writing is a part of Planemo documentation: https://planemo.readthedocs.org/en/latest/writing.html Planemo is a command line toolset aimed at helping tool developers like you getting their tools into

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

Hi Martin, I'll take a look at the tutorials, thanks! Att. On Mon, Dec 28, 2015 at 4:10 PM Martin Čech wrote: > Hello Léo, > > all tool are sincerely welcomed in the Galaxy Tool Shed. > > Good tutorial for tool writing is a part of Planemo documentation: >

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

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 wrote: > Hi Léo, > > idneed we have a small

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

Hi, I've found this Trello card ( https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more information about it? best, On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning wrote: > Hi, > > yes we had some idea, but nothing materialised so far. We started

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

Ok, thanks! Best regards, On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning 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

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

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

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

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

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

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

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

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