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Start an interactive job, with a walltime of 2 hours, 2000MB of memory.
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srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash |
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Create a working directory on scratch3 and change into the newly-created directory. For example, for user abc123, the working directory will be
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mkdir /n/scratch3/users/a/abc123/skewerFastQCHisat2StringtieBallgown
cd /n/scratch3/users/a/abc123/skewerFastQCHisat2StringtieBallgown |
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Copy some test data following this page: Build Folder Structures From Sample Sheet for rcbio NGS Workflows
Load necessary modules:
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module load gcc/6.2.0 python/2.7.12 rcbio/1. |
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1Copy the example skewerFastQCHisat2StringtieBallgown.sh bash script, and the ballgown.r R code:
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cp /n/app/rcbio/1.3. |
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13/bin/skewerFastQCHisat2StringtieBallgown.sh /n/app/rcbio/1.1/bin/ballgown.r . |
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Now you can modify the options as needed. For example, if you have single end data, you should add read length. Please reference the Hisat2 user manual if you have any questions.
To edit the Kallisto and Sleuth bash script:
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nano skewerFastQCHisat2StringtieBallgown.sh
nano ballgown.r |
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To test the pipeline run the following command. Jobs will not be submitted to the scheduler.
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runAsPipeline "skewerFastQCHisat2StringtieBallgown.sh -r mm10 -a /home/ld32/rcbioDev/data/skewer_adapters.fa" "sbatch -p short -t 2:0:0 -n 1 --mem 4G" noTmp
# this is test run |
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To run the pipeline:
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runAsPipeline "skewerFastQCHisat2StringtieBallgown.sh -r mm10 -a /home/ld32/rcbioDev/data/skewer_adapters.fa" "sbatch -p short -t 2:0:0 -n 1 --mem 4G" noTmp run 2>&1 | tee output.log
# notice here 'run 2>&1 | tee output.log' is added to the command |
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To understand how 'runAsPipeline' works, how to check output, how to re-run the pipeline, please visit: Run Bash Script As Slurm Pipeline
Now you are ready to run an rcbio workflow
To instead run the 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.