search

isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
16 stars 4 forks source link

What's up with the java install? #40

Closed Astahlke closed 2 years ago

Astahlke commented 2 years ago

I can bypass this error by loading the java module on ceres. 

/project/ag100pest/conda_envs/polishCLR/lib/jvm/bin/java: symbol lookup error: /project/ag100pest/conda_envs/polishCLR/lib/jvm/bin/java: undefined symbol: JLI_StringDup
NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:
 JAVA_CMD: /project/ag100pest/conda_envs/polishCLR/lib/jvm/bin/java
 NXF_OPTS:

Does envionment.yml need a fix?

Astahlke commented 2 years ago

@j23414 and @isugif - still getting this error. Any ideas?

j23414 commented 2 years ago

Haha, @Sivanandan and I were also running into that. Nextflow requires Java 11 or greater. We just added openjdk=11 to:

But it's not merged yet. Waiting until new Docker image is published to DockerHub.

If you're on HPC, might be able to add it manually:

conda activate  /project/ag100pest/conda_envs/polishCLR
conda install openjdk=11

# Then find the openjdk java executable
find /project/ag100pest/conda_env/polishCLR/ | grep "java$"
JAVA_HOME=`find /project/ag100pest/conda_env/polishCLR/ | grep "java$"`

# Check if nextflow finds java and runs normally, or if you're still getting the error.
nextflow -version

Nevermind, you got it. Yes, it's being added to environment.yml 😄