[Debian-med-packaging] Bug#867535: trimmomatic fails on spaces in filenames

[Redmar]

Package: trimmomatic
Version: 0.35+dfsg-1
Severity: normal
Tags: patch

Dear Maintainer,

There is an error in the wrapper for the java class, which means that
properly
quoted arguments (like "File name.extension") get expanded, and passed
as File name.extension

-- System Information:
Debian Release: stretch/sid
  APT prefers xenial-updates
  APT policy: (500, 'xenial-updates'), (500, 'xenial-security'), (500,
'xenial'), (100, 'xenial-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.4.0-83-generic (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages trimmomatic depends on:
ii  default-jre     2:1.8-56ubuntu2
ii  libjbzip2-java  0.9.1-3

trimmomatic recommends no packages.

trimmomatic suggests no packages.

-- no debconf information

--===============3715461592210098623==
Content-Type: text/x-diff; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Content-Disposition: attachment; filename="spaced_filenames.diff"

Index: trimmomatic/debian/bin/TrimmomaticPE
===================================================================
--- trimmomatic.orig/debian/bin/TrimmomaticPE
+++ trimmomatic/debian/bin/TrimmomaticPE
@@ -8,4 +8,4 @@ if [ "" = "$JARVERSION" ] ; then
     exit 1
 fi
 
-java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCTIONTOCALL
$@
+java -classpath "$JARVERSION" org.usadellab.$PKGNAME.$FUNCTIONTOCALL
"$@"