These are chat archives for nextflow-io/nextflow

18th
Apr 2019
Paolo Di Tommaso
@pditommaso
Apr 18 07:09
@tobsecret Any env var is imported as NF var, therefore w/o \, like any other variable
@KochTobi nope, the only chance is resuming the execution provided no processes will be re-executed
KennethLim314
@KennethLim314
Apr 18 07:48
Is there currently an idiomatic way to mount EFS volumes using the aws-batch executor? I've tried the cloud.sharedstorageID earlier to no effect
Paolo Di Tommaso
@pditommaso
Apr 18 11:58
Nextflow 19.04 is out!
sureshhewa
@sureshhewabi
Apr 18 13:24
I want to run a python script under python 3.6.0.
I was using beforeScript "set +u; conda env create -f $PWD/environment.yml" to run the conda environment.
But I get CondaValueError: prefix already exists Error
for some reason --force or -f option is not working for me
Then I used: beforeScript "set +u; conda env remove -y -n python_3.6.0; conda env create -f $PWD/environment.yml"
afterScript "set +u; conda deactivate"
KochTobi
@KochTobi
Apr 18 13:26
I think -f stands for file
sureshhewa
@sureshhewabi
Apr 18 13:28
ohhh
so is this command is correct then?
beforeScript "set +u; conda env create -f $PWD/environment.yml --force"
KochTobi
@KochTobi
Apr 18 13:32
nextflow creates the conda environment for you if you provide it with the environment.yml file. https://www.nextflow.io/docs/latest/conda.html
sureshhewa
@sureshhewabi
Apr 18 13:33
I tried to do that, but had some issues
let me get back to you
if I use this command:
conda '/Users/myname/path/environment.yml'
.command.run: line 57: activate: No such file or directory
sureshhewa
@sureshhewabi
Apr 18 13:39
why it cannot fine "activate" ?
*why it cannot find "activate" ?
KochTobi
@KochTobi
Apr 18 13:40
try running the nextflow workflow from within a conda environment. It tries to execute source activate environmentname
sureshhewa
@sureshhewabi
Apr 18 13:41
I did that too
oh sorry I tried that to deactivate
should I do it after the conda line?
conda '/Users/myname/path/environment.yml'
source activate environmentname
?
KochTobi
@KochTobi
Apr 18 13:43
dummyuser@dummyhost:~$ conda activate
(base) dummyuser@dummyhost:~$ nextflow run ...
sureshhewa
@sureshhewabi
Apr 18 13:45
I got it. This may be a foolish question. I am running this on cluster environment. If I activate conda environment, will that get affected to other process?
KochTobi
@KochTobi
Apr 18 13:46
nextflow creates the environment in the workflow work directory so I don't think so
sureshhewa
@sureshhewabi
Apr 18 13:53
Thanks a lot!
sureshhewa
@sureshhewabi
Apr 18 14:04
I am installing "ratelimit" package from pip while I am creating the environment
name: python_3.6.0
dependencies:
  • python=3.6.0
  • requests
  • pip
  • pip:
    • ratelimit
I cannot use a pre defined environment. therefore I need to run it on run time
sureshhewa
@sureshhewabi
Apr 18 14:09
So the command I gave :
conda env create -f $PWD/environment.yml
conda env create -f $PWD/environment.yml --force
This command has now installed ratelimit-2.2.1 package. but when it run the nextflow, still it cannot find the package
I tried this has well"
conda env create -f $PWD/environment.yml --force
conda activate python_3.6.0
sureshhewa
@sureshhewabi
Apr 18 14:28
It seems that I need to restart shell
Tobias "Tobi" Schraink
@tobsecret
Apr 18 14:29
@pditommaso :pray: Thank You!
Tobias "Tobi" Schraink
@tobsecret
Apr 18 17:07
OMG the new ansi logging is so beautiful :heart_eyes:
Paolo Di Tommaso
@pditommaso
Apr 18 18:15
:+1: