Test with latest bowtie is failing

[tillea]

Hi,
there is an issue reported to the Debian bug tracker, which uncovers a problem with bowtie 1.1.2:

------------- EXCEPTION -------------
MSG: /usr/bin/bowtie call crashed: There was a problem running /usr/bin/bowtie : Encountered a space parsing the quality string for read r1
If this is a FASTQ file with integer (non-ASCII-encoded) qualities, please
re-run Bowtie with the --integer-quals option.
Command: bowtie-align --wrapper basic-0 -e 70 -l 28 -n 2 -S --12 t/data/bowtie/reads/e_coli.cb t/data/bowtie/indexes/e_coli /tmp/ILc9j2LRpw/aBsCFOfFVE.sam

STACK Bio::Tools::Run::WrapperBase::_run /build/bioperl-run-1.7.2/blib/lib/Bio/Tools/Run/WrapperBase/CommandExts.pm:1032
STACK Bio::Tools::Run::Bowtie::run /build/bioperl-run-1.7.2/blib/lib/Bio/Tools/Run/Bowtie.pm:358
STACK toplevel t/Bowtie.t:234
-------------------------------------

I think the issue occures since there is no such executable bowtie-align any more. The executables that are shipped with bowtie are named bowtie-align-l or bowtie-align-s. I personally have no idea which one is the right one to run the test.
Kind regards, Andreas.