Bowtie2 site-specific tweaks for fastq_screen with Bowtie2

SciLifeLab / facs

Fast and Accurate Classification of Sequences using Bloom filters

http://facs.scilifelab.se/

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Closed brainstorm closed 10 years ago

brainstorm commented 10 years ago

Unfortunately it uses UPPMAX-specific path to refer to the bowtie2 index. There is no Galaxy rsync indexes for those organisms, yet.
Correct with statement for backwards compat with python 2.6.6.
Cleanup and re-running benchmarks with @guillermo-carrasco fixes for memory_profiling and simNGS read trimming.