> De : David Eccles (gringer) [david.ecc...@mpi-muenster.mpg.de]
> Date d'envoi : 11 juillet 2011 05:16
> À : denovoassembler-users@lists.sourceforge.net
> Objet : [Denovoassembler-users] Quick test run of Ray using phiX genome
> 
> I've managed to get a quick automated test-run of Ray working. It should
> take less than 30s to finish (6s on my desktop computer).
> 
> This currently only works using the released versions of Ray... I'm
> having a bit of trouble with the git versions (both my fork and seb's
> fork). Hopefully this test will help with tracking down those bugs.
> 
> $ sh test_phiX.sh
> Checking full Ray run with phiX genome... phiX sequence downloaded...
> 10000 Reads simulated... Running Ray... success (match in forward
> direction)!
> 
> Here's a summary of the steps:
> 1) use esearch/efectch to get the phiX genome (NC_001422)
> 2) use readSimulator/VirtualNextGenSequencer to simulate reads from genome
> 3) run Ray with 2 processors (so message-passing is used)
> 4) search/grep for scaffold output in original genome sequence
> 5) search/grep for scaffold output in reverse complement of original
> genome sequence
> 
> This assumes that test_phiX.sh is running from a directory inside the
> main Ray source directory (e.g. unit-tests).
> 
> For the script to work 'out of the box', you'll need wget to download
> the genome, and grep together with the fastx tools (fastx-toolkit in
> debian/ubuntu, or http://hannonlab.cshl.edu/fastx_toolkit/) in order to
> get the final search working (especially reverse-complement).
> 
> Git commit is here:
> 
> https://github.com/gringer/ray/commit/d6e3d989c4a141debea8295663a01343976bfae8
> 
> -- David Eccles (gringer)
> 
> Denovoassembler-users mailing list
> Denovoassembler-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
> 

Looks like a good system test.

                                                     Sébastien

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