These are chat archives for nextflow-io/nextflow

2nd
May 2017
Maxime Garcia
@MaxUlysse
May 02 2017 07:57
Hi, I'm catching up with what happened since friday.
Is docker.runOptions = '-u $(id -u):$(id -g)' similar to docker.fixOwnership = true ?
Or did I misunderstood its purpoise ?
@globor Travis is really easy to set up especially with docker set up.
You should not have any problems, given what you already did ;-)
Paolo Di Tommaso
@pditommaso
May 02 2017 07:59
the final result it supposed to be the same, but it's achieved in a different manner
docker.fixOwnership = true runs chown command after the task execution setting the setting owner
Maxime Garcia
@MaxUlysse
May 02 2017 08:00
I see
Paolo Di Tommaso
@pditommaso
May 02 2017 08:01
-u $(id -u):$(id -g) is supposed to work properly, but I've seen strange failures when a tool rely on the $HOME variable
Maxime Garcia
@MaxUlysse
May 02 2017 08:02
ok
I'll keep docker.fixOwnership = true then, thanks
Paolo Di Tommaso
@pditommaso
May 02 2017 08:04
Yes, I think it's safer
by default $HOME=/root in the container
but specifying -u $(id -u):$(id -g) it becomes $HOME=/
Maxime Garcia
@MaxUlysse
May 02 2017 08:06
I can see why it could be a problem
Félix C. Morency
@fmorency
May 02 2017 13:23
@pditommaso when using a scratch, where is the named pipe created? Shared FS or local on node?
Paolo Di Tommaso
@pditommaso
May 02 2017 13:24
local
Félix C. Morency
@fmorency
May 02 2017 13:25
AH! That might explain why it's working with some of our pipelines :D
Paolo Di Tommaso
@pditommaso
May 02 2017 13:25
ah
why ?
Félix C. Morency
@fmorency
May 02 2017 13:26
There seem to be issues with named pipe and samba on the latest FreeNAS
Paolo Di Tommaso
@pditommaso
May 02 2017 13:26
!
local storage is not the machine disk ?
Félix C. Morency
@fmorency
May 02 2017 13:27
Yup. Should work in that case
Félix C. Morency
@fmorency
May 02 2017 14:09
Yeah it works with the scratch
Wonderful
Paolo Di Tommaso
@pditommaso
May 02 2017 14:11
:)
Félix C. Morency
@fmorency
May 02 2017 15:02
I don't know if it's a "nf issue", but nf just hangs there and do nothing when there are issues with named pipe perms
jobs are scheduled than it runs indef.
Paolo Di Tommaso
@pditommaso
May 02 2017 15:03
um
what kind of problem with named pipes ?
Félix C. Morency
@fmorency
May 02 2017 15:04
write permission denied
(this is related to the samba issue, but it has impact of nf's behaviour). just wanted you to know
Paolo Di Tommaso
@pditommaso
May 02 2017 15:06
let me check a thing
Paolo Di Tommaso
@pditommaso
May 02 2017 15:17
@fmorency Since I'm unable to replicate the problem, can you give a try with the snapshot I've just upload ?
NXF_VER=0.24.4-SNAPSHOT nextflow run .. etc
Félix C. Morency
@fmorency
May 02 2017 15:18
Will do
Félix C. Morency
@fmorency
May 02 2017 18:41
@pditommaso what's the proper citation now?
Ah yeah got it on GH. You should also put it in the NF documentation :P