> 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 ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users