These are chat archives for nextflow-io/nextflow

27th
May 2015
Andrew Stewart
@andrewcstewart
May 27 2015 16:48
hey @pditommaso I think I may have found a bug in how nextflow is running docker
the $PWD does not seem to be actually mounting in the container
Paolo Di Tommaso
@pditommaso
May 27 2015 16:57
Can you manage to reproduce and open an issue on Github please?
Andrew Stewart
@andrewcstewart
May 27 2015 16:58
Yes, but im first trying to narrow down to a few possibilities
and am wondering if any such issues have been coming up in general
Paolo Di Tommaso
@pditommaso
May 27 2015 17:00
It never happend to me
Andrew Stewart
@andrewcstewart
May 27 2015 17:02
at this point im wondering if im having some kind of trouble mounting following a symlink
Paolo Di Tommaso
@pditommaso
May 27 2015 17:04
I would suggest to change to work dir and try to execute the .command.run
Andrew Stewart
@andrewcstewart
May 27 2015 17:18
aha
Ok, I wouldn't necessarily file this as a bug
but more as a word of warning
to those using docker
Paolo Di Tommaso
@pditommaso
May 27 2015 17:19
symlink issue ?
Andrew Stewart
@andrewcstewart
May 27 2015 17:19
dont try to symlink to your workdir :)
yeah
Paolo Di Tommaso
@pditommaso
May 27 2015 17:20
in other words you were using as workDir a symlink ?
Andrew Stewart
@andrewcstewart
May 27 2015 17:20
I have my workdir symlinked into the directory where im running my pipelines from.. so instead I did 'nextflow run -w /work'
and when I do that, the .command.run invokes Docker with "-v /work:/work"
I started on that blog post for you btw.
Paolo Di Tommaso
@pditommaso
May 27 2015 17:21
wow, that great!
Andrew Stewart
@andrewcstewart
May 27 2015 17:21
Im thinking a collection of 'lessons learned' may be valuable to others
such as this
Paolo Di Tommaso
@pditommaso
May 27 2015 17:21
a lot !
do you have your own blog? otherwise we can host you
Andrew Stewart
@andrewcstewart
May 27 2015 17:24
I do but we can just cross post it
mine is just for my own personal technical notes, I dont think anyone reads it :D
Paolo Di Tommaso
@pditommaso
May 27 2015 17:25
:)
however I will add some warning about using symlinks with docker
thanks to remind me that