generateCMDmappingCondorProject_Diag TruSight01 2014 07 03

pcus572:~ yvans$ perl /Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current/generateCMDmappingCondor.pl

#######################

The script you are running now is only for Research purpose and for no other purpose.

#######################

1, Please copy all the fastq files from run folder to /condor_sh/projects; the folder structure should be the same as the original run folder, e.g. Project_excap/Sample_excap1/*.fastq.gz

2, Log into Tor as root,

change the permission by: chmod -R 777 Project_excap

change owner, group as SBSUser by: chown -R SBSUser:SBSUser Project_excap

3, log out from root

If you haven't done the above, you can stop this script now and run it again when it is ready, otherwise press return

After all the files have been transferred, Input the project name, in this case - Project_excap

Project_Diag-TruSight01-2014-07-03

Making the folder structure in the condor required data structure and generate mapping commands (saved in commandMapping.bash under each sample/data) ......

A sample configuration file (sampleMac.conf) is also generated in the same folder to start further analysis after alignment A group configuration file (groupMac.conf) is generated under the Project folder, which can be used for running analysis on a batch of samples

Please input the full path to the diagnosticBundle, the default is "/Volumes/data.odin/diagnosticBundle" if you just press return

Please input the full path to the dataDistro, the default is "/Volumes/data.odin/diagnosticBundle/refData/dataDistro_r01_d01_diag" if you just press return

Please input the full path to the script folder (git local copy), the default is "/Volumes/data.odin/diagnosticBundle/script/amg/variantcalling/pipeline/pipeline_current" if you just press return

Please input the full path to the software folder, the default is "/Volumes/data.odin/diagnosticBundle/tools" if you just press return

Now you can go into tor and run each commandMapping.bash file

Good Luck!

pcus572:~ yvans$