These are chat archives for nextflow-io/nextflow

2nd
Sep 2015
Rahul
@RahulReddy75
Sep 02 2015 12:19
Hello @pditommaso
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:20
hey there
Rahul
@RahulReddy75
Sep 02 2015 12:20
hi...
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:20
still facing problems with parallelisation ?
Rahul
@RahulReddy75
Sep 02 2015 12:21
So the same issue exists... nextflow with docker multiple containers...
yes... i do not know how to create multiple containers...
i would like to see a example if possible...
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:21
what do you mean exactly by multiple containers
multiple instances of the same Docker image
of multiple processes using a different Docker images
?
Rahul
@RahulReddy75
Sep 02 2015 12:22
may be different images in different containers
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:22
um
let's say you have pipeline having two processes, for example:
Rahul
@RahulReddy75
Sep 02 2015 12:23
ok
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:24
procss A {
  '''
  foo
  '''
}

process B {
  '''
  bar
  '''
}
Rahul
@RahulReddy75
Sep 02 2015 12:24
ok
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:25
you can execute them with two different docker images adding the in the nextflow.config the following settings
process.$A.container = 'docker/image1'
process.$B.container = 'docker/image2'
it is explained here
is that fine?
Rahul
@RahulReddy75
Sep 02 2015 12:28
yes i did go through that... but my doubt is... with reference to the example i mentioned earlier... how can i run blast process and extract process in different containers... What image should i have in those containers..?
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:30
by extract process, do you mean execute processes ?
Rahul
@RahulReddy75
Sep 02 2015 12:31
Yes
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:32
don't you know what container exactly to use?
you should create a Docker image containing the tools used in that script: blast, t_coffee, etc
otherwise you could simply use the ones we provide in the examples, that is nextflow/examples
thus, execute docker pull nextflow/examples in your terminal
and add process.container = 'nextflow/examples' in your nextflow.config file
Rahul
@RahulReddy75
Sep 02 2015 12:36
ok i will try it
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:37
have you had a look to this blog post?
http://www.nextflow.io/blog/2014/nextflow-meets-docker.html
there it is explained
Rahul
@RahulReddy75
Sep 02 2015 12:39
yes i did..
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:43
so what is not working ?
Rahul
@RahulReddy75
Sep 02 2015 12:47
that method is working perfectly... but the only issue is i had to run processes in different containers.. i did not how i do that..
Paolo Di Tommaso
@pditommaso
Sep 02 2015 12:52
could you explain me in detail what do you mean by that ?