tmp/oncodrivefml_sge.R

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

devtools::load_all('/imppc/labs/lplab/share/marc/repos/ergWgsTools')

input <- '/imppc/labs/lplab/share/marc/insulinomas/processed/hg38/oncodrive/vcf/strelka2/variants_sub.tsv'
elements <- file.path(getwd(),'elements.tsv')
output_dir <- file.path(getwd())
dir.create(output_dir,
           showWarnings = FALSE)
configuration <- '/imppc/labs/lplab/share/marc/insulinomas/processed/hg38/oncodrive/oncodriveFML/oncodrivefml_v2.conf'
cores = 10
name = paste0('FML_', basename(getwd()))
queue = 'imppcv3'
log = '/imppc/labs/lplab/share/marc/insulinomas/logs'

script = paste0('export LC_ALL=C.UTF-8\n',
                'export LANG=C.UTF-8\n',
                'source /software/debian-8/general/virtenvs/oncodriveCLUSTL-v1.1.1-py3/bin/activate\n',
                paste('Rscript /imppc/labs/lplab/share/marc/repos/ergWgsTools/tmp/oncodrivefml.R',
                      input,
                      elements,
                      output_dir,
                      configuration))

email = 'clusterigtpmsubirana@gmail.com'
RtoSge::toSge(cores = cores,
              name = name,
              queue = queue,
              log = log,
              script = script,
              email = email)