These are chat archives for nextflow-io/nextflow

5th
Jul 2017
Michael Milton
@TMiguelT
Jul 05 2017 02:02
@pditommaso (re DNAnexus) Yep, I followed those instructions.
$ jar -tf resources/opt/nextflow/framework/0.25.2/nextflow-0.25.2-dx.jar | grep dx
dxfs-0.5.3.jar
So the dxfs jar is being included in the nextflow jar. It's just not being loaded for some reason
I can make a github issue about this. But I know it's not officially supported so
Paolo Di Tommaso
@pditommaso
Jul 05 2017 06:19
when you are getting the error java.lang.IllegalArgumentException: Cannot a find a file system provider for scheme: dxfs
keep in mind you will be able to access dxfs protocol only having the dnanexus properly configured eg. launching a NF application in the DNAnexus cloud
Michael Milton
@TMiguelT
Jul 05 2017 06:23
This is inside DNAnexus
Paolo Di Tommaso
@pditommaso
Jul 05 2017 06:24
weird, it looks it's not using the right NF package
Michael Milton
@TMiguelT
Jul 05 2017 06:26
Wrong version? Or it isn't compiling correctly?
Paolo Di Tommaso
@pditommaso
Jul 05 2017 06:28
I think I found the problem
change NXF_PACKAGE with NXF_MODE
make sure to modify the script that's uploaded with the app bundle
not having access any more to DNAnexus service, this feature is not tested anymore
likely there could be other problems
Michael Milton
@TMiguelT
Jul 05 2017 06:50
Thanks! I'll try that out
Michael Milton
@TMiguelT
Jul 05 2017 07:10
Now I'm getting
CAPSULE EXCEPTION: Capsule /opt/nextflow/framework/0.25.2/nextflow-0.25.2-one.jar does not have mode dx (for stack trace, run with -Dcapsule.log=verbose)
USAGE: java -jar ../../opt/nextflow/framework/0.25.2/nextflow-0.25.2-one.jar <options> <path or Maven coords of application JAR/capsule>
Paolo Di Tommaso
@pditommaso
Jul 05 2017 07:11
we can conclude that it's not working, I'm sorry
Michael Milton
@TMiguelT
Jul 05 2017 07:15
No worries
Paolo Di Tommaso
@pditommaso
Jul 05 2017 07:16
you can still package NF apps like any other application as DX bundles, tho won't take advantage of cloud scaling
Michael Milton
@TMiguelT
Jul 05 2017 07:18
Unfortunately the cloud scaling stuff is farily important
But that's fine, I was just exploring NF, I understand why you don't want to support DNAnexus
Félix C. Morency
@fmorency
Jul 05 2017 13:47
@pditommaso Quick question. Do you have an ETA for #399? I want to know if I need to implement a workaround in the mean time.
Paolo Di Tommaso
@pditommaso
Jul 05 2017 13:48
I was doing some dev now
Félix C. Morency
@fmorency
Jul 05 2017 13:49
:D
Félix C. Morency
@fmorency
Jul 05 2017 15:33
@pditommaso how do I test it again?
Félix C. Morency
@fmorency
Jul 05 2017 15:55
found. It works
Paolo Di Tommaso
@pditommaso
Jul 05 2017 16:07
Nice
Vote! ;)
Anthony Underwood
@aunderwo
Jul 05 2017 16:47
Hi. Quick question re installation for multiple users
When installing a directory ~/.nextflow is created containing capsule, framework and tmp subdirs.
How can I install nextflow for all users on the system?
I also find that on a lustre file storage system I get this error
Launching `tutorial.nf` [happy_wing] - revision: 893fda69d5
ERROR ~ Can't open cache DB: /phengs/hpc_storage/home/anthony/projects/nextflow_test/.nextflow/cache/f0bbef1e-3a63-4f70-9209-5eb46c1e550a/db

Nextflow needs to run in a file system that supports file locks.
As workaround you can launch it from local directory and specify
the work directory in the shared file system by using by `-w` command line option.
Paolo Di Tommaso
@pditommaso
Jul 05 2017 16:55
Some lustre users reported this problem, there's a thread in the NF Google group
I think I need to mount it with lock support
mount -t lustre -o flock..
Regarding the installation, NF home path is defined by the NXF_HOMEvariable
Félix C. Morency
@fmorency
Jul 05 2017 17:37
Can I vote if I don't have a twitter account?
Paolo Di Tommaso
@pditommaso
Jul 05 2017 20:31
You don't have a Twitter account ?! What's wrong with you? :D
Félix C. Morency
@fmorency
Jul 05 2017 20:33
ikr