feat: add trimmomatic to tools/ #192
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Are you sure this is necessary? biocontainers should have added a trimmomatic executable to the $PATH, as that's what they usually do. It should be unneeded to invoke the full path here.
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I was trying to work out access to the executable, but without cd'ing to the exact directory I wasn't able to get it to work
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That's likely because it's being called with java. There is a utility wrapper script at /usr/local/bin/trimmomatic that provides the functionality and is on PATH. So you should be able to swap java -jar trimmomatic.jar with trimmomatic and remove the directory change.
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Thank you @adthrasher! Hadn't noticed that distinction
a-frantz
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