These are chat archives for nextflow-io/nextflow

6th
Feb 2015
Sascha Steinbiss
@satta
Feb 06 2015 11:48
hmmm... is there any way to have nextflow get the environment variables in a docker container?
Paolo Di Tommaso
@pditommaso
Feb 06 2015 11:51
@satta Sorry I bit busy now. However I'm not getting what your goal
Sascha Steinbiss
@satta
Feb 06 2015 11:52
I'm running a pipeline inside a docker container. this container sets its own $PATH to point at software installed inside
Paolo Di Tommaso
@pditommaso
Feb 06 2015 11:52
Could you please post it in the nextflow forum
Sascha Steinbiss
@satta
Feb 06 2015 11:52
ok
no hurry!
Paolo Di Tommaso
@pditommaso
Feb 06 2015 12:51
@satta but also nextflow run in the container or only the nextflow processes ?
Sascha Steinbiss
@satta
Feb 06 2015 13:34
only the process, with -with-docker
on mac os x, using boot2docker-vm
Paolo Di Tommaso
@pditommaso
Feb 06 2015 13:34
ok
Sascha Steinbiss
@satta
Feb 06 2015 13:34
I will write up a more detailed question later and post it to the google group
Paolo Di Tommaso
@pditommaso
Feb 06 2015 13:35
however environment variables defined in the nextflow.config file or in this way
are exported in the container
OK
:)
Sascha Steinbiss
@satta
Feb 06 2015 13:36
I need the other way around -- $PATH set in the container (ENV PATH ... in the Dockerfile) should be propagated to the pipeline
Paolo Di Tommaso
@pditommaso
Feb 06 2015 13:39
this is weird it's not even possible in BASH
Sascha Steinbiss
@satta
Feb 06 2015 13:40
I'll try to get a better grip on the problem and post later, thanks anyway :)
Paolo Di Tommaso
@pditommaso
Feb 06 2015 13:40
ok