Description Usage Arguments Details Value Examples
fastq-dump to dump SRA file.
1 2 3 4 5 | run_fq_dump(filepath = "/group/jrigrp4/BS_teo20/WGBS",
slurmsh = "slurm-script/dump_WGBS.sh", rmsra = TRUE, email = NULL)
run_fq_dump2(filepath = "/group/jrigrp4/BS_teo20/WGBS", rmsra = TRUE,
gzip = TRUE, email = NULL, run = c(TRUE, "bigmemh", "8196", "1"))
|
filepath |
The absolute path of the SRA files. |
slurmsh |
File name of the output shell command. |
rmsra |
Remove the original SRA file after dumpping. |
email |
Your email address that farm will email to once the job was done/failed. |
gzip |
GZIP the fastq files. |
run |
Parameters control the array job partition. A vector of c(TRUE, "bigmemh", "8196", "1"): 1) run or not, 2) -p partition name, 3) –mem, adn 4) –ntasks. |
see more detail about SRA with Aspera downloading: http://www.ncbi.nlm.nih.gov/books/NBK158899/#SRA_download.downloading_sra_data_using
return a single shell script to run.
1 2 3 4 5 6 | ## run a single node job:
run_fq_dump(filepath="/group/jrigrp4/BS_teo20/WGBS",
slurmsh="slurm-script/dump_WGBS.sh", rmsra=TRUE, email=NULL)
## run array job:
run_fq_dump2(filepath="test", rmsra=TRUE, gzip=TRUE, email=NULL, run=c(TRUE, "bigmemh", "8196", "1"))
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