Description Usage Arguments Details Value Examples
fastq-dump to dump SRA file.
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inputdf |
sra files in df as input. no need path info. [df, df["sra"]] |
runnum |
Number of running jobs in parallel. [int, =100] |
dumppath |
The absolute path of the SRA files to dump. [chr, "largedata/dump/"] |
rmsra |
Remove the original SRA file after dumpping. [logical, =TRUE] |
gzip |
GZIP the fastq files. [logical, =FALSE] |
email |
Your email address that farm will email to once the job was done/failed. [chr, "y@gmail.com"] |
slurmsh |
File name of the output shell command. [chr, ="slurm-script/run_dump_"] |
runinfo |
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.
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