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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 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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ls -l group*/*/ group2/normal3/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558212/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558212/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558212/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558212/anotherTwoMillionReads_1.fq group2/normal2/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558210/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558210/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558210/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558210/anotherTwoMillionReads_1.fq group2/normal1/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558208/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558208/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558208/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group2/ERR558208/anotherTwoMillionReads_1.fq group1/tumor3/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR558211/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR558211/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR558211/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR558211/anotherTwoMillionReads_1.fq group1/tumor2/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435855/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435855/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435855/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435855/anotherTwoMillionReads_1.fq group1/tumor1/: total 16K lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435830/twoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 80 Jan 16 11:59 lib1_lane2_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435830/twoMillionReads_1.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_2.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435830/anotherTwoMillionReads_2.fq lrwxrwxrwx 1 ld32 ld32 87 Jan 16 11:59 lib1_lane1_1.fq -> /n/shared_db/misc/rcbio/data/fruitFlyFastq/group1/ERR435830/anotherTwoMillionReads_1.fq |
Now you are ready to run an rcbio workflow
To instead run workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.
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