These are chat archives for nextflow-io/nextflow

30th
Aug 2018
Michael Epstein
@miepstei
Aug 30 2018 12:37
following on from @aunderwo 's question, I have a similar docker in nxf question. I notice from examining the .command.run that the entrypoint for the docker container is set. Is there any way to get the .command.sh file to include -l for the bash login? The reason I am asking is that my docker image has binaries installed that are not on the path by default (its set in .bashrc). Or is the recommended solution just to install into standard dirs already on the PATH by default?
Paolo Di Tommaso
@pditommaso
Aug 30 2018 12:38
is it related to this nextflow-io/nextflow#850 ?
anyhow the recommended solution is definitely to install your tool on the default container PATH
Michael Epstein
@miepstei
Aug 30 2018 12:42
I think the latter is a better solution as I need to source the .bashrc file within the container. Thanks for your help!
Paolo Di Tommaso
@pditommaso
Aug 30 2018 12:43
:+1:
Shellfishgene
@Shellfishgene
Aug 30 2018 14:07
I have a conceptual question I'm still not sure about: If I have process that get files via 3 input channels, I have to make sure all 3 files are from the same sample and not mixed. Do I have to do this by combining the channels into one first (using by:0 on a sample ID for example), and then getting three files from one channel, or is there a way to do this in the input: section of the process?
micans
@micans
Aug 30 2018 15:05
I've been running NXF_VER=0.32.0-SNAPSHOT nextflow run, and this started failing this afternoon with Java Runtime errors and a problematic frame in C [libc.so.6+0x149f46] (after having run without problems for well over two weeks). Just checking there is no chance this has anything to do with NF or groovy ... when I run that snapshot, will it always run identical code?
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:10
too bad
when I run that snapshot, will it always run identical code?
what do you mean ?
micans
@micans
Aug 30 2018 15:13
I mean, I ran NXF_VER=0.32.0-SNAPSHOT nextflow run about 30 times (with different parameters). On the nextflow side, is it always the exact same version of code that is run? That is what I expect, I'm just crossing off unlikely possibilities.
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:14
the same version of which code? :)
NF code?
micans
@micans
Aug 30 2018 15:15
Yes the NF code, not our pipeline project code
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:15
if you are using the same NF version is the the same code ..
micans
@micans
Aug 30 2018 15:16
OK .. I assume that using that same SNAPSHOT prefix implies I am using the same NF version, right?
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:17
well, snapshots may change you should check the build number
micans
@micans
Aug 30 2018 15:17
OK thanks :-)
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:18
however that kind error is very unusual, I've only seen when there's not enough local storage
micans
@micans
Aug 30 2018 15:19
mmm. I just freed up 6T. Still maybe something I need to check; two hours ago I had a disk quota problem.
Surprised by the way that local storage would lead to a bus error (which this is)
But I know little about these things
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:20
they ways (to crash) of the JVM are infinite :satisfied:
micans
@micans
Aug 30 2018 15:20
hehe
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:21
@Shellfishgene yes, but not the combine produces a cartesian product, I guess you may need join or groupTuple
micans
@micans
Aug 30 2018 15:23
can I include a build number in NXF_VER ?
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:24
nope :(
micans
@micans
Aug 30 2018 15:26
OK, I'll poke around. The snapshot with groupKey() has worked fab for me.
Interesting. It seems somehow non-random. It first worked, and now it fails. I've tried log out/log in, more memory .. I might remove the nextflow assets cache, or I'll try running a different project. Voodoo bug hunting.
Shellfishgene
@Shellfishgene
Aug 30 2018 15:28
@pditommaso I'm using combine with by, that seems to do the same thing as join.
Paolo Di Tommaso
@pditommaso
Aug 30 2018 15:31
if there's not repetition for the same key it should be the same
Yasset Perez-Riverol
@ypriverol
Aug 30 2018 23:46
Hi all @pditommaso, Is nextflow using any Web GUI for tracing jobs, and job logs?