I'm trying to set up gkno but have come across some errors on the way when trying the run-test pipeline.
First time it stopped at the build-reference task and then reported the error "/bin/sh: /"pathonmycomputer"/gkno/gkno_launcher/tools/MOSAIK/bin/MosaikBuild: No such file or directory" I looked into named folder and realized that it was empty. To resolve this i placed the bin files from the latest Mosaikbuild into this directory which seemed to solve the problem. Is this a possible bug that anyone else has seen?
When retrying after replacing the files everything runs smoothly until the sort-multiple-bam-step. Gkno then reports "Error 1" and in the error log i find "bamtools sort ERROR: could not open /"pathonmycomputer"/gkno/gknolauncher/simulatedreads1.multiple.bam for reading... Aborting." There is no file called simulatedreads_1.multiple.bam in the project folder either. I'm a bit stuck here, has anyone else seen this error?
I'm test running this on Mac OSX 10.8.2 and it's gkno version 0.42. My java version is 1.6.0_37 so that shouldn't be a problem.