[Debian-med-packaging] Bug#671813: Bashism in tophat2 that prevents to run on systems where dash is default.

[Charles Plessy]

Package: tophat
Version: 2.0.0-1
Severity: grave

Hi all,

/usr/bin/tophat2 is a shell script (#!/bin/sh), but uses command(s?) available
only with bash.

  $ tophat2 
  /usr/bin/tophat2: 13: [[: not found

This is probably easy to solve, but I did not have time to choose
which is the most ecosystem-friendly solution.

Cheers,

-- Charles

-- System Information:
Debian Release: wheezy/sid
  APT prefers stable
  APT policy: (910, 'stable'), (900, 'testing'), (800, 'unstable'), (500, 'stable-updates'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.39-bpo.2-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages tophat depends on:
ii  bowtie2                   2.0.0-beta5-1  ultrafast memory-efficient short r
ii  dpkg                      1.16.0.3       Debian package management system
ii  libboost-thread1.49.0     1.49.0-2       portable C++ multi-threading
ii  libc6                     2.13-21        Embedded GNU C Library: Shared lib
ii  libgcc1                   1:4.7.0-6      GCC support library
ii  libstdc++6                4.7.0-6        GNU Standard C++ Library v3
ii  python                    2.6.6-14       interactive high-level object-orie
ii  zlib1g                    1:1.2.6.dfsg-1 compression library - runtime

tophat recommends no packages.

Versions of packages tophat suggests:
ii  bowtie                        0.12.7-3   ultrafast memory-efficient short r
ii  cufflinks                     1.3.0-1    Transcript assembly, differential 

-- no debconf information