These are chat archives for nextflow-io/nextflow

14th
Aug 2017
Anthony Underwood
@aunderwo
Aug 14 2017 12:50
Hi. When Singularity is used with Nextflow it's stripping out the host environment (.command.run reveals the -ue option is used). Is there a way to ask it to not do this? - I need it to use host proxy ENV variables
Paolo Di Tommaso
@pditommaso
Aug 14 2017 13:01
if you define them in the nextflow.config file it should work, eg
env {
  FOO = 'bar'
}
Anthony Underwood
@aunderwo
Aug 14 2017 13:17
Cool - that worked :)
Paolo Di Tommaso
@pditommaso
Aug 14 2017 13:19
nice
NF enforces containers isolation to guarantee the pipeline portability
therefore env variable must be defined in the config file
Simone Baffelli
@baffelli
Aug 14 2017 15:49
Good evening. Has anybody ever experience any trouble with nextflow clean -before UUID
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:51
what kind of problem ?
Simone Baffelli
@baffelli
Aug 14 2017 15:51
I get a not-so-useful error: ERROR ~ Unexpected error [EOFException]
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:52
try to re-execute as
Simone Baffelli
@baffelli
Aug 14 2017 15:52
sudo?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:52
nextflow -log <file> clean .. etc
and share the log file
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:54
umm, corrupted index ?
Simone Baffelli
@baffelli
Aug 14 2017 15:54
:scream:
any chance to rescue it?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:57
little chances .. :/
Simone Baffelli
@baffelli
Aug 14 2017 15:57
:scream:
no disk space left :(
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:58
ah
Simone Baffelli
@baffelli
Aug 14 2017 15:58
I hope i manage to copy it on our server and work from there
I don't want to wait for a couple of days again
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:58
this explains it . .
Simone Baffelli
@baffelli
Aug 14 2017 15:58
but that is the reason why I wanted to cleanup
Paolo Di Tommaso
@pditommaso
Aug 14 2017 15:59
try to clean-up one UUID at time
instead of -before
Simone Baffelli
@baffelli
Aug 14 2017 15:59
that works
tomorrow will be a very long day
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:00
no holidays ?!?
Simone Baffelli
@baffelli
Aug 14 2017 16:00
why?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:00
well, it's 15 Aug ... but yes, stupid question :)
Simone Baffelli
@baffelli
Aug 14 2017 16:01
:smile: no sadly not here
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:01
ohh
Simone Baffelli
@baffelli
Aug 14 2017 16:01
in former times most people were not catholic here
therefore no holiday
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:02
all catholic holidays are former pagan celebrations .. :)
Simone Baffelli
@baffelli
Aug 14 2017 16:02
but the protestant are famously anti-holiday
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:02
I see
Simone Baffelli
@baffelli
Aug 14 2017 16:02
the famous calvinist work ethic
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:03
hence, I left some comments here
Simone Baffelli
@baffelli
Aug 14 2017 16:13
I don't see them
I found a very lazy way to delete all old runs!! Long live grep and shell pipes
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:14
you should have received a GH notification now
Simone Baffelli
@baffelli
Aug 14 2017 16:15
I saw it, you are right
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:15
ok
Simone Baffelli
@baffelli
Aug 14 2017 16:15
shall I change it?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:15
it would help
Simone Baffelli
@baffelli
Aug 14 2017 16:16
But not today :sunglasses:
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:16
no pb!
Simone Baffelli
@baffelli
Aug 14 2017 16:16
tomorrow perhaps. I suppose you will have holidays?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:17
yep!
Paolo Di Tommaso
@pditommaso
Aug 14 2017 16:49
@baffelli I've uploaded 0.25.7-SNAPSHOT that should handle better that error
Simone Baffelli
@baffelli
Aug 14 2017 17:51
Very good! What did you change exactly?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 17:53
just handling the exception to avoid the execution stop
have u tried it ?
Simone Baffelli
@baffelli
Aug 14 2017 18:50
No, I went home, will test tomorrow
So, in principle you just skip delting those runs that cannot be removed?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 19:03
Yes
Simone Baffelli
@baffelli
Aug 14 2017 19:09
I will try tomorrow, meanwhile I used grep to pipe the runs into a file and then deleting them individually looping through the list
Paolo Di Tommaso
@pditommaso
Aug 14 2017 19:10
+1
Ido Tamir
@idot
Aug 14 2017 20:41
Hi, I have a bunch of R and Rmd files in bin and the 1. one is found, but then when I try to source the other ones, it fails. Any advice besides building a package?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 20:42
when I try to source the other ones
what do you mean exactly ?
Ido Tamir
@idot
Aug 14 2017 20:45
in makeKnit .R: knit("analysis.Rmd") in analysis.Rmd: source("analysis.R")
makeKnir.R works, but then analysis.Rmd is not found because its of course not in the work folder but in the bin folder.
Paolo Di Tommaso
@pditommaso
Aug 14 2017 20:47
I guess R resolve import against the current path
but when execute from NF it is executed from a different folder, hence it's unable to find that script
Ido Tamir
@idot
Aug 14 2017 20:48
yes exacty.
Paolo Di Tommaso
@pditommaso
Aug 14 2017 20:49
I'm not a R expert but there should be a way to specify the path where look for scripts
Ido Tamir
@idot
Aug 14 2017 20:51
Is it possible to declare a bin file as an input file and have it being copied to the process work folder?
Paolo Di Tommaso
@pditommaso
Aug 14 2017 20:52
yes, but it's a bit ugly, I would suggest to investigate how to make your R script path independent
Ido Tamir
@idot
Aug 14 2017 20:53
ok thanks a lot!
Paolo Di Tommaso
@pditommaso
Aug 14 2017 20:55
the NF project dir is given by baseDir, see for example
you can use it to define the path where look for R scripts