Galaxy tools for docking protein-compounds.
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. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi
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/
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 Galaxy and the Tool Shed. Also have a look at https://github.com/galaxyproject/tools-iuc for tool writing inspiration and http://galaxy-iuc-standards.readthedocs.org/en/latest/ for best practices. Let us know if we can help. Thank you for using Galaxy. M. On Mon, Dec 28, 2015 at 12:58 PM Léo Biscassi <leo.biscassi@gmail.com> wrote:
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. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi ___________________________________________________________ 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/
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@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
Hi Martin, I'll take a look at the tutorials, thanks! Att. On Mon, Dec 28, 2015 at 4:10 PM Martin Čech <marten@bx.psu.edu> wrote:
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 Galaxy and the Tool Shed. Also have a look at https://github.com/galaxyproject/tools-iuc for tool writing inspiration and http://galaxy-iuc-standards.readthedocs.org/en/latest/ for best practices.
Let us know if we can help.
Thank you for using Galaxy.
M.
On Mon, Dec 28, 2015 at 12:58 PM Léo Biscassi <leo.biscassi@gmail.com> wrote:
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. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi
___________________________________________________________
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
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@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/
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 <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@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
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@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@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/
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? Best regards, On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning <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@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
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@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
Am 28.12.2015 um 19:29 schrieb Léo Biscassi: 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
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@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@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
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@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
Am 28.12.2015 um 19:29 schrieb Léo Biscassi: 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/ >
Ok, thanks! Best regards, On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
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
Am 28.12.2015 um 20:33 schrieb Léo Biscassi: 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@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@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
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@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
Am 28.12.2015 um 19:29 schrieb Léo Biscassi: 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
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@gmail.com> wrote:
Ok, thanks!
Best regards,
On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
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
Am 28.12.2015 um 20:33 schrieb Léo Biscassi: 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@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@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@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/ >>> >>
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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? [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/dockin... Att. On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <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@gmail.com> wrote:
Ok, thanks!
Best regards,
On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning <bjoern.gruening@gmail.com> wrote:
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
Am 28.12.2015 um 20:33 schrieb Léo Biscassi: 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@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@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@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/ >>>> >>> >
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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 'add awesome autodock tools' 5) push your changes to your fork with - git push origin autodock <- this is your branch name 6) go to github and create a PR against my galaxytools repository Oh this exciting! Thanks! Bjoern Am 30.01.2016 um 19:44 schrieb Léo Biscassi:
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@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@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@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@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@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/ >>>>>>> >>>>>> >>>> >>
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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/dockin...
Att.
On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <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@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@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@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@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@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/ >>>>>>> >>>>>> >>>> >>
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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@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/dockin...
Att.
On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <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@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@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@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@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@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/ >>>>>>> >>>>>> >>>> >>
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-- *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
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@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@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/dockin...
Att.
On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <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@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@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@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@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@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
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@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@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/dockin... > > Att. > > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <leo.biscassi@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@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@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@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@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@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
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 <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@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@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/dockin...
Att.
On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <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@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@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@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@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@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
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 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@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@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@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/dockin... > > Att. > > On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <leo.biscassi@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@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@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@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@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@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
participants (4)
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Bjoern Gruening -
Björn Grüning
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Léo Biscassi -
Martin Čech