Ubuntu
trimmomatic package

Trimmomatic{SE,PE} cannot handle white spaces in file names

Bug #1558602 reported by Sebastian Jaenicke on 2016-03-17

This bug report is a duplicate of: Bug #1702235: trimmomatic fails on spaces in filenames. Edit Remove

This bug affects 1 person

Affects		Status	Importance	Assigned to	Milestone
	trimmomatic (Ubuntu)	New	Undecided	Unassigned

Bug Description

The provided shell wrappers /usr/bin/Trimmomatic{SE,PE} don't account for white spaces in file names.

Solution:

-java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCNAME $@
+java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCNAME "$@"

Revision history for this message

Hans Joachim Desserud (hjd) wrote on 2017-07-12:

Thanks for taking your time to report this issue and help making Ubuntu better.

I'm marking this as a duplicate of bug 1702235, since they both discuss the same issue, but it contains more details and additional information. Please look at the other bug report to see if there is any missing information that you can provide, or to see if there is a workaround for the bug. Additionally, any further discussion regarding the bug should occur in the other report. Feel free to continue to report any other bugs you may find.