Bowtie2 index shouldn't be hardcoded - Githubissues

SciLifeLab / facs

Fast and Accurate Classification of Sequences using Bloom filters

http://facs.scilifelab.se/

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Bowtie2 index shouldn't be hardcoded #121

Closed guillermo-carrasco closed 10 years ago

guillermo-carrasco commented 10 years ago

Right now, bowtie2 indexes are hardcoded so that the tests can run in UPPMAX:

https://github.com/SciLifeLab/facs/blob/master/tests/test_fastqscreen.py#L51

Instead of doing this, a better approach would be to:

Look for the indexes in Galaxy as the other ones are being fetched and
If the fetching fails, build the indexes and store them following the same directory structure than the other indexes