These are chat archives for nextflow-io/nextflow

20th
Aug 2016
Evan Floden
@evanfloden
Aug 20 2016 09:50
What is the default precedence with regards to executables in $baseDir/bin versus in environment PATH?
Paolo Di Tommaso
@pditommaso
Aug 20 2016 10:05
it's prepended to $PATH
thus it has priority over other paths
Evan Floden
@evanfloden
Aug 20 2016 11:03
I just wonder what is best practice for Docker-based workflows for when they are to be are run without docker? Ideally I would like have the prerequisite executables in $baseDir/bin (for running without Docker) and have the Docker installed binaries take precedence when running with Docker.
Paolo Di Tommaso
@pditommaso
Aug 20 2016 11:09
um
interesting point, but the best practice is to not put the binaries in the bin folder, only scripts
also because distributing compiled binaries is very unreliable
Evan Floden
@evanfloden
Aug 20 2016 11:14
So have a prerequisite software section in the README telling people what to install? I agree distributing compiled binaries is not reliable, but it is so easy, usually works and therefore tempting for my lazy part. Point taken though, I will avoid doing this in the future! Thanks mate
Paolo Di Tommaso
@pditommaso
Aug 20 2016 11:15
I think the best way is to say pre-requisite are JVM + Nextflow + Docker (optional)
if you don't have Docker see the Dockerfile for configuration details
the dockerfile is self-explanatory and unambiguous and what to do
Evan Floden
@evanfloden
Aug 20 2016 11:17
an optional pre-requisite! Very true for the Docker config. How about a little script which coverts the Dockerfile into an ‘install.sh’ like script?
Paolo Di Tommaso
@pditommaso
Aug 20 2016 11:18
!
I think there are a couple of project trying to implement the little script you are proposing :)
but I don't remember the name now
Evan Floden
@evanfloden
Aug 20 2016 11:19
Really!? Gets a bit circular though
Paolo Di Tommaso
@pditommaso
Aug 20 2016 11:20
as long you give a precise description of the dependencies the installation it's a user problem
(going to sail now, there's a good wind!)
:sailboat::sailboat::sailboat::sailboat:
Evan Floden
@evanfloden
Aug 20 2016 11:22
Enjoy it mate! I’ve been for a swim and watching the All Blacks smashing Australia :rugby_football: Talk later
Paolo Di Tommaso
@pditommaso
Aug 20 2016 11:23
:+1: