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Note: You can copy and paste all the text to your Linux command line to run. Anything with "#" is comment, and will be IGNORED by Linux.
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# Make a directory in scratch3scratch file system and work there. We recommend creating separate folders for each project. mkdir -p /n/scratch3scratch/users/${USER:0:1}/$USER/test && cd /n/scratch3scratch/users/${USER:0:1}/$USER/test |
Note: Each user has 10 25 TiB /n/scratch3scratch space. There is no backup for data saved in/n/scratch3scratch, and files will be deleted if they are not accessed for a month. You can read more about /n/scratch3scratch on the Filesystems page.
Copy testing sample sheet to work directory
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The sample sheet is in Microsoft Excel format. You can look at this file by transferring it to your local computer, and opening in Excel. Programs that can be used to transfer the sample sheet include Filezilla or WinSCP. For help on transferring files to or from the O2 cluster, please read the File Transfer wiki page.
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You can also use our new O2Portal to do file transfer: https://o2portal.rc.hms.harvard.edu/pun/sys/dashboard
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Load related modules
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module load gcc/6.2.0 python/2.7.12 rcbio/1.3.13 |
Build folder structure from the sample sheet
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