Align cut and raw contigs to set of references
1 2 | cmdwrap.align.contigs.with.ref(indir.cut, indir.raw, outdir, reffile = NA,
batch.n = NA, batch.id = NA)
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | #
# create multiple runs on HPC using the command line version
#
## Not run:
#DATA <- SET THIS DIRECTORY
indir.cut <- paste(DATA, 'contigs_150408_unaligned_cut', sep='/' )
indir.raw <- paste(DATA, 'contigs_150408_unaligned_raw', sep='/' )
outdir <- paste(DATA, 'contigs_150408_wref', sep='/' )
batch.n <- 200
tmp <- data.table(FILE=list.files(indir.raw, pattern='fasta$', recursive=T))
tmp[, BATCH:= ceiling(seq_len(nrow(tmp))/batch.n)]
tmp <- tmp[, max(BATCH)]
for(batch.id in seq.int(1,tmp))
{
cmd <- cmdwrap.align.contigs.with.ref(indir.cut, indir.raw, outdir, batch.n=batch.n, batch.id=batch.id)
cmd <- cmd.hpcwrapper(cmd, hpc.nproc= 1, hpc.q='pqeelab', hpc.walltime=1, hpc.mem="5000mb")
cat(cmd)
cmd.hpccaller(paste(DATA,"tmp",sep='/'), paste("hrct",paste(strsplit(date(),split=' ')[[1]],collapse='_',sep=''),sep='.'), cmd)
}
## End(Not run)
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