christos proukakis

so I am also unable to run this on our main server Linux any help will be very welcome! bash novoBreak_distribution_v1.1.3rc/run_novoBreak.sh novoBreak_distribution_v1.1.3rc/novoBreak hg19.fasta bamfiles/P38_14.MB2.sorted.dup_removed.q40.bam bamfiles/P38_14CER.sorted.dup_removed.q40.bam 2 -PWD readlink: invalid option -- 'P' Try 'readlink --help' for more information. mkdir: missing operand Try 'mkdir --help' for more information. novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line 26: /home/rmgtcpr/novoBreak_distribution_v1.1.3rc/novoBreak/novoBreak:...

So i see that readlink is a problem, and i did brew install coreutils so i can use greadlink, and I edited the file changing readlink to greadlink everywhere i also did brew install perl in case that was the problems now I get someting to do with symlinks which someone commented on, probably beyond me to solve... greadlink: invalid option -- 'P' Try 'greadlink --help' for more information. usage: mkdir [-pv] [-m mode] directory ... /Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh: line...

Hello I would really like to use this, but 1) I am trying on a single core i7 mac with 16 G of RAM. Is there any chance it will work, even it takes days, or should I give up? 2) it doesnt wan to start- am i doing this the right way? bash /Volumes/SD/novoBreak_distribution_v1.1.3rc/run_novoBreak.sh /SD/novoBreak_distribution_v1.1.3rc /Volumes/SD/bwa0712/hg19.fasta /Volumes/SD/MPS_work/P38_14.MB2.sorted.dup_removed.q40.bam /Volumes/Toshiba4Tb/WGSdata/mayo_MPS/P38_14.MB2.sorted.dup_removed.q40.chr4.sorted.bam...