Funannotate Installation : How to configure funannotate app find the Trimmomatic program?

[jacob-israel]

Are you using the latest release?
Yes , I am using the latest funannotate version.

Describe the bug
funanotate does not find trimmomatic when running the funannotate check command, how can I configure or tell funanotate where trimmomatic is located?

What command did you issue?
funannotate check --show-versions

Logfiles
ERROR: trimmomatic not installed

OS/Install Information

• Ubuntu Linux Server 24.04 LTS
• output of funannotate check --show-versions

[hyphaltip]

You need the program trimmomatic to be in your $PATH when you run funannotate command.

What does this report in your environment?
which trimmomatic

[jacob-israel]

@hyphaltip trimmomatic is a java jar, trimmomatic-0.39.jar, at this moment it is in the PATH but it cannot be found, what should the java jar be like so that funannotate can find it? I don't have a trimmomatic binary file

[jacob-israel]

@hyphaltip I made a bash script with the following code:

$ cat trimmomatic
#!/bin/bash

/data2TB/apps/jdk-22.0.2/bin/java -jar /data2TB/apps/Trimmomatic-0.39/trimmomatic-0.39.jar

and then $chmod a+x to the trimmomatic bash script but it doesn't work

Is there any trimmomatic binary program?

[hyphaltip]

I believe the funannotate check is assuming the conda installed version -
which is this code linked below which does some checking on java version for wrapping I believe

• https://github.com/bioconda/bioconda-recipes/tree/master/recipes/trimmomatic
• this is the script https://github.com/bioconda/bioconda-recipes/blob/master/recipes/trimmomatic/trimmomatic.py

This is the build script for the trimmomatic conda which takes that python script and renames it as an executable script
cp $RECIPE_DIR/trimmomatic.py $outdir/trimmomatic

See
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/trimmomatic/build.sh

[hyphaltip]

This may be annoying as it assumes a conda installed trimmomatic but I think it was a way to ensure some uniformity in how java would be called?