What is the difference between picard and picard-tools ?

Question

[takoyaki]

Hey, everyone. Does anyone know the difference between picard and picard-tools ?

I think we use picard like java -jar picard.jar ~

However, in my text book, we can install picard-tools like brew install picard-tools and use like picard SortSam or picard MarkDuplicates.

"picard" is operated indirectly by java, while the latter is operated directly by command.

Are these the same ? or completely different program ? Also, do you know how to install picard-tools without using homebrew ? ( I use linux OS, so I can't use homebrew )

Thanks.

Answer 1

[i.sudbery]

They are the same program. Its just in the latter case someone has built a bash script which inspects the command you give it and builts the appropriate java call. You can see this if you type

less `which picard`

[takoyaki]

Thanks. My problem become clear !