marvinParser: marvinParser

In msubirana/DNAseqPipeline: What the Package Does (One Line, Title Case)

Description

Parser for Marvin cluster Using this parser is possible to send jobs from host to Marvin cluster through ssh It is necessary generate a public and private key pair for an automatic scp

Usage

marvinParser(
  job_name,
  cores = 1,
  partition = "normal",
  memory = "8G",
  email = "[e-mail]",
  modules = NULL,
  nodes = 1,
  script,
  tmp_sh,
  stdout,
  stderr
)

Arguments

job_name	Name of the job
cores	Cores to use
partition	partition where to run the script. By default 'partition'.
memory	Amount of RAM used per cpu. By default '8G'.
email	Email where to send notifications. By default '[e-mail]'
modules	List of modules to load. Check the once that you need using module av command in Marvin.
nodes	Number of nodes
script	Script to run
tmp_sh	File where to save the sh script in the host.
stdout	File where standard output output go. Standard output contains all the messages that your job has sent to the standard output messages, i.e. anything you see written.
stderr	File where standard error output go. Standard error contains all the messages that your job has sent to the error channel, i.e. “command not found”, “no such file or directory”…

Value

A job to Marvin cluster and the ib batch job as a message.

Examples

## Not run: 
bam <- '/gpfs42/projects/lab_lpasquali/shared_data/marc/epimutations/raw/wgs/hg37/toDo/10759.bam'
sample <- basename(gsub('.bam','',bam))
job_name <- paste0(sample, '_realignBwa')
script <- paste('Rscript /gpfs42/projects/lab_lpasquali/shared_data/marc/repos/DNAseqPipeline/tmp/realignBwaParser.R',
                bam,
                ref,
                out_dir,
                threads)

email <- '[e-mail]'
tmp_sh <- file.path('/home/msubirana', paste0(job_name,'.sh'))
memory <- '32G'
#' stdout <- file.path(out_dir, job_name)
stderr <- file.path(out_dir, job_name)

marvinParser(job_name=job_name,
             cores=cores,
             modules=modules,
             script=script,
             tmp_sh=tmp_sh,
             memory=memory,
             stdout=stdout,
             stderr=stderr)

## End(Not run)

msubirana/DNAseqPipeline documentation built on Dec. 21, 2021, 10:12 p.m.