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Posted to dev@taverna.apache.org by Nadeesh Dilanga <na...@gmail.com> on 2016/05/06 03:33:17 UTC
Trying to invoke docker image
Started go through existing work flows and use the tool activity plugin to
simple run a
docker.
Re: Trying to invoke docker image
Posted by Nadeesh Dilanga <na...@gmail.com>.
Hi Alan,
Don't forget that you can ask for help on this mailing list - or look on
> stackoverflow :)
>
Thanks, if I got an error in future I'll ask for help from this mailing
list. Earlier I looked only stackoverflow.
So you plan to initially have a tool service that runs curl?
>
First I want to test the REST API from a REST client (Chrome REST
client/curl). So I can test that API works fine. Then I can make a simple
java client api that invoke those rest calls. So I can use it inside the
taverna plugin.
Postman app is a good one too. I searched about it.
> Have you considered using a blogging site to describe your progress?
>
No, but I'll make a new post in my blog to describe my progress in this
project.
Hi Stian,
IT would be good if you could take some notes, say in a blog or in the
> Taverna wiki about the different possibilities for communicating with the
> Docker engine.
I started to update my blog with a new post about this project. I'll
include facts about "different possibilities for communicating with Docker
engine". It's good to share my knowledge about this project with the help
of my blog.
Let us know if you want access to
> https://cwiki.apache.org/confluence/display/TAVERNADEV - I believe Gale
> can grant you access once you have registered.
Thanks, but I'd like to update my blog with the new facts I learn from this
project. I'll send a message to dev@taverna mailing list with a link of my
blog post.
Hi Gale,
Just make sure you also send a message to the dev@taverna mailing list with a
> link to your blog post or wiki article. Thanks!
I'm still working on my new post about this project. After I complete it,
I'll send a message to dev@taverna mailing list with a link of my blog post.
It's nice to get help from you all. Thanks ! :)
On Mon, May 16, 2016 at 6:15 PM, Gale Naylor <Ga...@noventussolutions.com>
wrote:
> Just make sure you also send a message to the dev@taverna mailing list
> with
> a link to your blog post or wiki article. Thanks!
>
> On Mon, May 16, 2016, 5:36 AM Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
> > Hi! Thanks for your update.
> >
> > IT would be good if you could take some notes, say in a blog or in the
> > Taverna wiki about the different possibilities for communicating with
> > the Docker engine. I think we need to think about how it would work
> > on different operating systems and what needs to be set up to enable
> > Taverna to talk to Docker. E.g. in Windows and OSX you may have a
> > "docker" command line, but the docker engine runs on a Virtual Machine
> > with a different IP.
> >
> > (Let's not consider Windows 10 preview's native Docker for now)
> >
> > Let us know if you want access to
> > https://cwiki.apache.org/confluence/display/TAVERNADEV - I believe
> > Gale can grant you access once you have registered.
> >
> > On 15 May 2016 at 15:30, Nadeesh Dilanga <na...@gmail.com> wrote:
> > > Hi Stian,
> > >
> > > I tried many things these days. Here I focused on core parts of the
> > project.
> > > First I successfully built and run a simple workflow using 'FASTA'
> > service.
> > > Here I used 'Taverna Workbench Core 2.5.0' IDE.
> > > Then I run a existing docker image which is called 'hello-world' and
> got
> > an
> > > output like this 'Hello from Docker' etc.
> > > My next aim is to invoke docker through the REST API.
> > > I tried to enable REST API on Docker, but got an error. Now I'm fixing
> it
> > > and hope to finish it ASAP. When it done I'm ready to use Chrome REST
> > > client through the activity plugin with the help of curl commands.
> > > So then I can try these steps programmatically for the project.
> > > By the way right now, I'm creating a docker container and a docker
> image
> > > with the help of youtube videos. :)
> > >
> > > On Fri, May 6, 2016 at 4:46 PM, Stian Soiland-Reyes <st...@apache.org>
> > > wrote:
> > >
> > >> Great! If you are in Linux, you might have to add your user to the
> > >> "docker" user group and log in again, so that you don't need "sudo
> > >> docker" but can just do "docker".
> > >>
> > >> Note that this effectively gives your user root, as you could do
> > >>
> > >> docker run -v /:/root -it ubuntu chroot /root bash
> > >>
> > >> to get your real /
> > >>
> > >>
> > >> I think the Docker activity could use the Docker protocol, which I
> > >> think can be set up for authentication.. perhaps that could be an
> > >> advanced stage.. we'll probably need a README about how you need to
> > >> set up the Docker environment in order for your new Taverna activity
> > >> to play along with it.
> > >>
> > >> On 6 May 2016 at 04:33, Nadeesh Dilanga <na...@gmail.com> wrote:
> > >> > Started go through existing work flows and use the tool activity
> > plugin
> > >> to
> > >> > simple run a
> > >> > docker.
> > >>
> > >>
> > >>
> > >> --
> > >> Stian Soiland-Reyes
> > >> Apache Taverna (incubating), Apache Commons RDF (incubating)
> > >> http://orcid.org/0000-0001-9842-9718
> > >>
> >
> >
> >
> > --
> > Stian Soiland-Reyes
> > Apache Taverna (incubating), Apache Commons RDF (incubating)
> > http://orcid.org/0000-0001-9842-9718
> >
>
Re: Trying to invoke docker image
Posted by Gale Naylor <Ga...@noventussolutions.com>.
Just make sure you also send a message to the dev@taverna mailing list with
a link to your blog post or wiki article. Thanks!
On Mon, May 16, 2016, 5:36 AM Stian Soiland-Reyes <st...@apache.org> wrote:
> Hi! Thanks for your update.
>
> IT would be good if you could take some notes, say in a blog or in the
> Taverna wiki about the different possibilities for communicating with
> the Docker engine. I think we need to think about how it would work
> on different operating systems and what needs to be set up to enable
> Taverna to talk to Docker. E.g. in Windows and OSX you may have a
> "docker" command line, but the docker engine runs on a Virtual Machine
> with a different IP.
>
> (Let's not consider Windows 10 preview's native Docker for now)
>
> Let us know if you want access to
> https://cwiki.apache.org/confluence/display/TAVERNADEV - I believe
> Gale can grant you access once you have registered.
>
> On 15 May 2016 at 15:30, Nadeesh Dilanga <na...@gmail.com> wrote:
> > Hi Stian,
> >
> > I tried many things these days. Here I focused on core parts of the
> project.
> > First I successfully built and run a simple workflow using 'FASTA'
> service.
> > Here I used 'Taverna Workbench Core 2.5.0' IDE.
> > Then I run a existing docker image which is called 'hello-world' and got
> an
> > output like this 'Hello from Docker' etc.
> > My next aim is to invoke docker through the REST API.
> > I tried to enable REST API on Docker, but got an error. Now I'm fixing it
> > and hope to finish it ASAP. When it done I'm ready to use Chrome REST
> > client through the activity plugin with the help of curl commands.
> > So then I can try these steps programmatically for the project.
> > By the way right now, I'm creating a docker container and a docker image
> > with the help of youtube videos. :)
> >
> > On Fri, May 6, 2016 at 4:46 PM, Stian Soiland-Reyes <st...@apache.org>
> > wrote:
> >
> >> Great! If you are in Linux, you might have to add your user to the
> >> "docker" user group and log in again, so that you don't need "sudo
> >> docker" but can just do "docker".
> >>
> >> Note that this effectively gives your user root, as you could do
> >>
> >> docker run -v /:/root -it ubuntu chroot /root bash
> >>
> >> to get your real /
> >>
> >>
> >> I think the Docker activity could use the Docker protocol, which I
> >> think can be set up for authentication.. perhaps that could be an
> >> advanced stage.. we'll probably need a README about how you need to
> >> set up the Docker environment in order for your new Taverna activity
> >> to play along with it.
> >>
> >> On 6 May 2016 at 04:33, Nadeesh Dilanga <na...@gmail.com> wrote:
> >> > Started go through existing work flows and use the tool activity
> plugin
> >> to
> >> > simple run a
> >> > docker.
> >>
> >>
> >>
> >> --
> >> Stian Soiland-Reyes
> >> Apache Taverna (incubating), Apache Commons RDF (incubating)
> >> http://orcid.org/0000-0001-9842-9718
> >>
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Trying to invoke docker image
Posted by Stian Soiland-Reyes <st...@apache.org>.
Hi! Thanks for your update.
IT would be good if you could take some notes, say in a blog or in the
Taverna wiki about the different possibilities for communicating with
the Docker engine. I think we need to think about how it would work
on different operating systems and what needs to be set up to enable
Taverna to talk to Docker. E.g. in Windows and OSX you may have a
"docker" command line, but the docker engine runs on a Virtual Machine
with a different IP.
(Let's not consider Windows 10 preview's native Docker for now)
Let us know if you want access to
https://cwiki.apache.org/confluence/display/TAVERNADEV - I believe
Gale can grant you access once you have registered.
On 15 May 2016 at 15:30, Nadeesh Dilanga <na...@gmail.com> wrote:
> Hi Stian,
>
> I tried many things these days. Here I focused on core parts of the project.
> First I successfully built and run a simple workflow using 'FASTA' service.
> Here I used 'Taverna Workbench Core 2.5.0' IDE.
> Then I run a existing docker image which is called 'hello-world' and got an
> output like this 'Hello from Docker' etc.
> My next aim is to invoke docker through the REST API.
> I tried to enable REST API on Docker, but got an error. Now I'm fixing it
> and hope to finish it ASAP. When it done I'm ready to use Chrome REST
> client through the activity plugin with the help of curl commands.
> So then I can try these steps programmatically for the project.
> By the way right now, I'm creating a docker container and a docker image
> with the help of youtube videos. :)
>
> On Fri, May 6, 2016 at 4:46 PM, Stian Soiland-Reyes <st...@apache.org>
> wrote:
>
>> Great! If you are in Linux, you might have to add your user to the
>> "docker" user group and log in again, so that you don't need "sudo
>> docker" but can just do "docker".
>>
>> Note that this effectively gives your user root, as you could do
>>
>> docker run -v /:/root -it ubuntu chroot /root bash
>>
>> to get your real /
>>
>>
>> I think the Docker activity could use the Docker protocol, which I
>> think can be set up for authentication.. perhaps that could be an
>> advanced stage.. we'll probably need a README about how you need to
>> set up the Docker environment in order for your new Taverna activity
>> to play along with it.
>>
>> On 6 May 2016 at 04:33, Nadeesh Dilanga <na...@gmail.com> wrote:
>> > Started go through existing work flows and use the tool activity plugin
>> to
>> > simple run a
>> > docker.
>>
>>
>>
>> --
>> Stian Soiland-Reyes
>> Apache Taverna (incubating), Apache Commons RDF (incubating)
>> http://orcid.org/0000-0001-9842-9718
>>
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718
Re: Trying to invoke docker image
Posted by Alan Williams <al...@googlemail.com>.
On 15-May-16 15:30, Nadeesh Dilanga wrote:
> Hi Stian,
Hello
> I tried many things these days. Here I focused on core parts of the project.
> First I successfully built and run a simple workflow using 'FASTA' service.
> Here I used 'Taverna Workbench Core 2.5.0' IDE.
> Then I run a existing docker image which is called 'hello-world' and got an
> output like this 'Hello from Docker' etc.
Great.
> My next aim is to invoke docker through the REST API.
> I tried to enable REST API on Docker, but got an error. Now I'm fixing it
Don't forget that you can ask for help on this mailing list - or look on
stackoverflow :)
> and hope to finish it ASAP. When it done I'm ready to use Chrome REST
> client through the activity plugin with the help of curl commands.
I use the PostMan app.
So you plan to initially have a tool service that runs curl?
> So then I can try these steps programmatically for the project.
> By the way right now, I'm creating a docker container and a docker image
> with the help of youtube videos. :)
Youtube is an excellent source of technical videos.
Have you considered using a blogging site to describe your progress?
Alan
Re: Trying to invoke docker image
Posted by Nadeesh Dilanga <na...@gmail.com>.
Hi Stian,
I tried many things these days. Here I focused on core parts of the project.
First I successfully built and run a simple workflow using 'FASTA' service.
Here I used 'Taverna Workbench Core 2.5.0' IDE.
Then I run a existing docker image which is called 'hello-world' and got an
output like this 'Hello from Docker' etc.
My next aim is to invoke docker through the REST API.
I tried to enable REST API on Docker, but got an error. Now I'm fixing it
and hope to finish it ASAP. When it done I'm ready to use Chrome REST
client through the activity plugin with the help of curl commands.
So then I can try these steps programmatically for the project.
By the way right now, I'm creating a docker container and a docker image
with the help of youtube videos. :)
On Fri, May 6, 2016 at 4:46 PM, Stian Soiland-Reyes <st...@apache.org>
wrote:
> Great! If you are in Linux, you might have to add your user to the
> "docker" user group and log in again, so that you don't need "sudo
> docker" but can just do "docker".
>
> Note that this effectively gives your user root, as you could do
>
> docker run -v /:/root -it ubuntu chroot /root bash
>
> to get your real /
>
>
> I think the Docker activity could use the Docker protocol, which I
> think can be set up for authentication.. perhaps that could be an
> advanced stage.. we'll probably need a README about how you need to
> set up the Docker environment in order for your new Taverna activity
> to play along with it.
>
> On 6 May 2016 at 04:33, Nadeesh Dilanga <na...@gmail.com> wrote:
> > Started go through existing work flows and use the tool activity plugin
> to
> > simple run a
> > docker.
>
>
>
> --
> Stian Soiland-Reyes
> Apache Taverna (incubating), Apache Commons RDF (incubating)
> http://orcid.org/0000-0001-9842-9718
>
Re: Trying to invoke docker image
Posted by Stian Soiland-Reyes <st...@apache.org>.
Great! If you are in Linux, you might have to add your user to the
"docker" user group and log in again, so that you don't need "sudo
docker" but can just do "docker".
Note that this effectively gives your user root, as you could do
docker run -v /:/root -it ubuntu chroot /root bash
to get your real /
I think the Docker activity could use the Docker protocol, which I
think can be set up for authentication.. perhaps that could be an
advanced stage.. we'll probably need a README about how you need to
set up the Docker environment in order for your new Taverna activity
to play along with it.
On 6 May 2016 at 04:33, Nadeesh Dilanga <na...@gmail.com> wrote:
> Started go through existing work flows and use the tool activity plugin to
> simple run a
> docker.
--
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons RDF (incubating)
http://orcid.org/0000-0001-9842-9718