These are chat archives for nextflow-io/nextflow

13th
May 2016
Paolo Di Tommaso
@pditommaso
May 13 2016 06:36
@jbyars It could, it depends on the default resource caps defined in your sge installation
Szilveszter Juhos
@szilvajuhos
May 13 2016 10:38
Is there an easy way to access the logging mechanism, i.e. writing entries into .nextflow.log ?
Paolo Di Tommaso
@pditommaso
May 13 2016 10:39
Of course
log.info|warn|error
Szilveszter Juhos
@szilvajuhos
May 13 2016 10:42
thanks, that was easy ;)
Paolo Di Tommaso
@pditommaso
May 13 2016 10:43
that's nextflow approach :)
Szilveszter Juhos
@szilvajuhos
May 13 2016 10:52
and is it guaranteed that if there are three processes writing to the same logfile, the messages will not be garbled?
I need to store the actual state of processes somewhere, so though writing into logs is the easiest for now
Paolo Di Tommaso
@pditommaso
May 13 2016 11:24
Um, it's not designed for that. Have you tried the trace file feature? http://www.nextflow.io/docs/latest/tracing.html#execution-report
Szilveszter Juhos
@szilvajuhos
May 13 2016 11:26
yes, it is what I need I guess
Paolo Di Tommaso
@pditommaso
May 13 2016 11:26
great!
Szilveszter Juhos
@szilvajuhos
May 13 2016 11:28
it takes some time to run stuff on this laptop, but apparently the trace file just does what I need, and I do not have to write an elaborate state-databse thingy
Paolo Di Tommaso
@pditommaso
May 13 2016 11:29
good
Stephen J Newhouse
@snewhouse
May 13 2016 16:47
palying with condo. take a look at https://anaconda.org/sjnewhouse/nextflow and have a play
*conda
Paolo Di Tommaso
@pditommaso
May 13 2016 16:54
oh cool
this means that nxf can be installed with conda?
Stephen J Newhouse
@snewhouse
May 13 2016 17:12
yes indeed
Paolo Di Tommaso
@pditommaso
May 13 2016 17:12
great
:clap:
Stephen J Newhouse
@snewhouse
May 13 2016 17:13
my pleasure
:smile:
Paolo Di Tommaso
@pditommaso
May 13 2016 17:13
Do you have any project there using it?
Stephen J Newhouse
@snewhouse
May 13 2016 17:13
I plan on having a play
Paolo Di Tommaso
@pditommaso
May 13 2016 17:13
nice
for any help just ping here
Stephen J Newhouse
@snewhouse
May 13 2016 17:14
struggling to find time to port all our hacky pipelines to nextflow
and now pushing to conda and bioconda as much as possible
Paolo Di Tommaso
@pditommaso
May 13 2016 17:14
well, better to give a start one at time :)
Stephen J Newhouse
@snewhouse
May 13 2016 17:14
yup
have you all also seen the mulled project https://github.com/mulled/mulled ?
Paolo Di Tommaso
@pditommaso
May 13 2016 17:15
oh no, this is a new thing
what it does?
optimise the container building?
Stephen J Newhouse
@snewhouse
May 13 2016 17:16
automates docker builds of packages from condo, brew, linux etc interesting stuff
Paolo Di Tommaso
@pditommaso
May 13 2016 17:17
ah cool, I will give a try
Stephen J Newhouse
@snewhouse
May 13 2016 17:17
groovy
have a great weekend!
Paolo Di Tommaso
@pditommaso
May 13 2016 17:17
same!