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SMALT and Bowtie2 now reproducible

Hi all,

SMALT and Bowtie2 are now reproducible as well (in Git and Svn, respectively).
Please note that I needed to make some changes to Bowtie that change its output — in particular, build hostname, time and compiler are no longer recorded at compile time and hence can not be printed in the output of ‘bowtie2 --version’. I don’t think that changes a lot, but if anyone considers this a problem, I’d be happy to just set them to arbitrary values.


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