'How can I solve a Clobber error for the installation of Trimmomatic?
I'm trying to install Trimmomatic with Conda (Windows PC) but this is the error I see: CondaVerificationError: The package for trimmomatic located at C:\Users\Utente\anaconda3\pkgs\trimmomatic-0.39-hdfd78af_2 appears to be corrupted. The path 'share/trimmomatic' specified in the package manifest cannot be found.
ClobberError: The package 'defaults/win-64::openjdk-11.0.13-h2bbff1b_0' cannot be installed due to a path collision for 'library/bin/freetype.dll'. This path already exists in the target prefix, and it won't be removed by an uninstall action in this transaction. The path is one that conda doesn't recognize. It may have been created by another package manager.
Clobber error is repeated for other .dll files.
I have already tried "clean --all" and "update --all" but it doesn't work. I also tried to uninstall and install Conda and Python but nothing change. I thought the problem was the presence of multiple folders because I installed Conda more times but deleting every folder doesn't help me. I thank you in advance if you will help me.
Solution 1:[1]
I don't know what, but there seems to be somethin wrong with symbolic links inside the trimmomatic package that does not work under windows.
Try to create an environemnt with openjdk:
conda create -c conda-forge --override-channels -n trimmomatic openjdk
Then download the binary manually, extract it and then run
conda activate trimmomatic
java -jar Trimmomatic-0.39\trimmomatic-0.39.jar
Thereby, adjust Trimmomatic-0.39\trimmomatic-0.39.jar to point to the .jar file that is inside the folder that you have extracted from the downloaded .zip file
Sources
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Source: Stack Overflow
| Solution | Source |
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| Solution 1 |