These are chat archives for nextflow-io/nextflow

4th
Oct 2016
Mokok
@Mokok
Oct 04 2016 09:15
Hi, I'm trying to add a custom local executor. To make it easier i worked directly with nextflow sources (extending the existing LocalExecutor) and ran a gradlew pack. But changing the nextflow-0.xx.x.jar under .nexflow/framework doesn't seem to work : i get an "Unknown executor name" error when running a job. (I also put the Executor class name in the ProcessFactory executorsMap). Any trick i should know about that ? ^^
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:16
how do you launch it ?
Mokok
@Mokok
Oct 04 2016 09:17
the job ?
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:17
nextflow
Mokok
@Mokok
Oct 04 2016 09:18
./nextflow run ./projects/.../main.nf -profile custom
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:18
did you run make install ?
Mokok
@Mokok
Oct 04 2016 09:19
(where 'custom' is my profile with ' process.executor = 'custom' ')
mh nop, i didn't, as i edited it from windows.
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:20
ok, the easiest to compile and test is
make compile
(that's just a shortcut for gradle compile)
and then use
./launch.sh run <same cmd line as nextflow>
the executor can be specified on the cmd line
./launch.sh run .. -process.executor custom
OR
make compile pack install
./nextflow ..
I would suggest the first approach
Mokok
@Mokok
Oct 04 2016 09:24
okey, i was foolishly expecting my magic jar swap trick to work ^^
thank for the answer
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:25
let me know if you manage to run it
Mokok
@Mokok
Oct 04 2016 09:38
compile error
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:39
shit happens :)
Mokok
@Mokok
Oct 04 2016 09:39

./gradlew -q compile exportClasspath

FAILURE: Build failed with an exception.

  • What went wrong:
    Execution failed for task ':nxf-commons:compileGroovy'.

    Could not find tools.jar. Please check that /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.102-1.b14.el7_2.x86_64/jre contains a valid JDK installation.

  • Try:
    Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.
    make: * [compile] Erreur 1

Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:39
I guess u are using JRE instead of JDK
Mokok
@Mokok
Oct 04 2016 09:39
so i checked my java installation , and it seems ok
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:40
do you have javac ?
Mokok
@Mokok
Oct 04 2016 09:41
mh, strange
i'll make a new java install for a jdk, to be sure
download it and then set the JAVA_HOME var
Mokok
@Mokok
Oct 04 2016 09:47
my bad, forgot the -devel in the package name >_<
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:47
:+1:
Mokok
@Mokok
Oct 04 2016 09:47
now compiled
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:48
good!
Mokok
@Mokok
Oct 04 2016 09:50
run worked
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:50
great
Mokok
@Mokok
Oct 04 2016 09:51
many thanks ! :)
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:51
welcome
out of curiosity, what system targets your executor ?
Mokok
@Mokok
Oct 04 2016 09:53
none for now, but it could be used to dialog with a "message queue interface" (dunno if it's clear ^^)
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:54
ah interesting
fair enough
Mokok
@Mokok
Oct 04 2016 09:54
thus the receiver is supposed to be able to execute it, and answer
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:54
yep makes sense
enterprise stuff I guess
Mokok
@Mokok
Oct 04 2016 09:55
yep, i dig all i can to fit our needs (we are in a research phase)
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:56
cool enjoy it
there plenty of these message broker in the Java world, you have good chance
maybe Apache Camel could be related
Mokok
@Mokok
Oct 04 2016 09:59
could be RabbitMQ...we'll see ! :)
Thanks again
Paolo Di Tommaso
@pditommaso
Oct 04 2016 09:59
;)