# Kneaddata installed with conda is not available

**URL:** <https://forum.biobakery.org/t/kneaddata-installed-with-conda-is-not-available/4147>\
**Category:** KneadData\
**Created:** [October 2, 2022, 8:41am UTC](https://forum.biobakery.org/t/kneaddata-installed-with-conda-is-not-available/4147 "2022-10-02T08:41:09Z")\
**Posts on this page:** 1\
**Showing post:** 5

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**Author:** ![Ben\_Siranosian](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ben_siranosian/32/2286_2.png) [@Ben\_Siranosian](https://forum.biobakery.org/u/Ben_Siranosian)\
**Post date:** [July 5, 2023, 4:14pm UTC](https://forum.biobakery.org/t/kneaddata-installed-with-conda-is-not-available/4147/5 "2023-07-05T16:14:26Z")

</div>

I’ve come across this error as well. It is due to a conflict between the biobakery workflows and the conda install. If you look at the file `$MYENV/bin/trimmomatic` you can see it is just a plain text wrapper for a java file. The first comment is “Wrapper script for Java Conda packages that ensures that the java runtime”

However, biobakery\_workflows is trying to call this plain text file as the jar file, visible in the error message `Err: CRITICAL ERROR: Error executing: java -Xmx500m -jar $MYENV/bin/trimmomatic SE -threads 1 ...`

I found the jar file that the wrapper script is calling, and replaced the wrapper script with it. First I backed up the wrapper script so it can still be used with the command “trimmomatic\_cmdline”

```auto
cp $MYENV/bin/trimmomatic $MYENV/bin/trimmomatic_cmdline
ln -s $MYENV/share/trimmomatic/trimmomatic.jar $MYENV/bin/trimmomatic
ln -s $MYENV/share/trimmomatic/trimmomatic.jar $MYENV/bin/trimmomatic.jar

```

Then, you can use the tools as normal, and use `trimmomatic_cmdline` if needed.  
`$MYENV` should be replaced with the path to your conda environment.

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