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) ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
