# load data.table of predefined phyloscanner runs
data(runs_rakai_couples)
# setup input, output and working directories
pty.data.dir <- '/Users/Oliver/duke/2016_PANGEAphylotypes/data'
work.dir <- getwd()
out.dir <- getwd()
# link to phyloscanner.py
prog.pty <- '/work/or105/libs/phylotypes/phyloscanner.py'
# produce bash scripts for the first two phyloscanner runs only
pty.select <- 1:2
# define phyloscanner arguments
pty.args <- list( prog.pty=prog.pty,
prog.mafft='mafft',
prog.raxml='"raxmlHPC-AVX -m GTRCAT"',
data.dir=pty.data.dir,
work.dir=work.dir,
out.dir=out.dir,
alignments.file=system.file(package="phyloscan", "HIV1_compendium_AD_B_CPX_v2.fasta"),
alignments.root='REF_CPX_AF460972',
alignments.pairwise.to='REF_B_K03455',
window.automatic= '',
merge.threshold=0,
min.read.count=1,
quality.trim.ends=23,
min.internal.quality=23,
merge.paired.reads=TRUE,
no.trees=FALSE,
dont.check.duplicates=FALSE,
num.bootstraps=1,
all.bootstrap.trees=TRUE,
min.ureads.individual=NA,
win=c(800,2400,250,250),
keep.overhangs=FALSE,
duplicated.raw.threshold=3,
duplicated.ratio.threshold=1/200,
select=pty.select)
# generate bash scripts
pty.c <- phsc.cmd.phyloscanner.multi(runs_rakai_couples, pty.args)
# print first bash script to screen
pty.c[1,cat(CMD)]
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