Trouble with Pilon installation
Entering edit mode
4.9 years ago
Rox ★ 1.3k

Hello everyone !

I'm trying to polish my genome assembly, and for this I need to use Pilon (there other options from PacBio tools and software being unavailable). My problem is that I don't see anywhere some recommendations to install this tool.

I read the several sections form the wiki page : , but wasn't able to find it. I found an installation using conda that didn't worked for me.

The steps I accomplished so far, is cloning the pilon deposit from github in my computer. Then, I tried to launch the script, which gave me the following error :

Loutre:~/pilon$ ./ 
./ 14: ./ sbt: not found
ln: impossible de créer le lien symbolique «/home/loutre/lib/pilon/pilon-dev.jar»: Aucun fichier ou dossier de ce type

(It says that the file or directory does not exist, which is true in my case).

I think that I missing something. As it's a java source file, I thought about using jar with some other arguments, but there is no single indications in the, and there is so many .scala files in the directory src. I'm kind of lost here.

I saw that some users recommended Pilon to other people, someone also had the same trouble as me ( smkopac) in this post : How to install Picard/Pilons software and do variant call on a set of .sam files? when trying to run :

java -Xmx16G -jar lib/htsjdk-1.130.jar pilon --help

Any help or further informations that I may have missed will be really appreciated. I hope that this is not a stupid question.



polishing pilon installation • 5.7k views
Entering edit mode
4.9 years ago
Rox ★ 1.3k

I allow myself to add my own answer to this question, in case some other people wonder.

So, clone the deposit is probably not the way we should install Pilon.

I've ran successfully Pilon after directly the .jar file available here : and then typing on a terminal, where your jar file is located :

java -jar pilon-1.21.jar --help

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