ex_script.R
In rPlant: R interface to the Agave and Foundation API

require(rPlant)
require(ape)

Validate("username", "password")  # add your own username and password.

## We need wait times for the Wait function
minWait = 5 # seconds
maxWait = 1800 # 30 min in seconds

# Upload a file to the DE
data(DNA.fasta)
write.fasta(sequences = DNA.fasta, names = names(DNA.fasta), 
            file.out = "DNA.fasta")
UploadFile(local.file.name="DNA.fasta", filetype="FASTA-0")

data(PROTEIN.fasta)
write.fasta(sequences = PROTEIN.fasta, names = names(PROTEIN.fasta), 
            file.out = "PROTEIN.fasta")
UploadFile(local.file.name="PROTEIN.fasta", filetype="FASTA-0")


### Workflow One ###
myJobW1MuP <- Muscle("PROTEIN.fasta", aln.filetype="PHYLIP_PARS",
                     job.name="muscleWORKFLOW1")
Wait(myJobW1MuP[[1]], minWait, maxWait)
myJobW1PPP <- PHYLIP_Pars("phylip_pars.aln", file.path=paste("analyses/",
                          myJobW1MuP[[2]], sep=""), type="PROTEIN",
                          job.name="phylipWORKFLOW1")
Wait(myJobW1PPP[[1]], minWait, maxWait)
RetrieveJob(myJobW1PPP[[1]], c("outtree.nwk"))
read.tree(paste(getwd(), myJobW1PPP[[2]], "outtree.nwk", sep="/")) -> Tree1
plot(Tree1)



### Workflow Two ###
myJobW2MaP <- Mafft("PROTEIN.fasta", type="PROTEIN", job.name="mafftWORKFLOW2")
Wait(myJobW2MaP[[1]], minWait, maxWait)
myJobW2FaP <- Fasttree("mafft.fa", type="PROTEIN", file.path=paste("analyses/",
                       myJobW2MaP[[2]], sep=""), job.name="fasttreeWORKFLOW2")
Wait(myJobW2FaP[[1]], minWait, maxWait)
RetrieveJob(myJobW2FaP[[1]], c("fasttree.nwk"))
read.tree(paste(getwd(), myJobW2FaP[[2]], "fasttree.nwk", sep="/")) -> Tree2
plot(Tree2)



### Workflow Three ###
myJobW3CWD <- ClustalW("DNA.fasta", job.name="clustalwWORKFLOW3")
Wait(myJobW3CWD[[1]], minWait, maxWait)
myJobW3FaD <- Fasttree("clustalw2.fa", file.path=paste("analyses/",
                       myJobW3CWD[[2]], sep=""), job.name="fasttreeWORKFLOW3")
Wait(myJobW3FaD[[1]], minWait, maxWait)
RetrieveJob(myJobW3FaD[[1]], c("fasttree.nwk"))
read.tree(paste(getwd(), myJobW3FaD[[2]], "fasttree.nwk", sep="/")) -> Tree3
plot(Tree3)



### Workflow Four ###
myJobW4MuD <- Muscle("DNA.fasta", aln.filetype="PHYLIP_INT", job.name="muscleWORKFLOW4")
Wait(myJobW4MuD[[1]], minWait, maxWait)
myJobW4RD <- RAxML("phylip_interleaved.aln", file.path=paste("analyses/",
                   myJobW4MuD[[2]], sep=""), job.name="raxmlWORKFLOW4")
Wait(myJobW4RD[[1]], minWait, maxWait)
RetrieveJob(myJobW4RD[[1]], c("RAxML_bestTree.nwk"))
read.tree(paste(getwd(), myJobW4RD[[2]], "RAxML_bestTree.nwk", sep="/")) -> Tree4
plot(Tree4)



### Or if you want to do all four workflows at the same time (in parallel), ###
### to do them more quickly do something like this:                         ###

### These first four can be run because they don't depend on each other ###
# myJobW1MuP <- Muscle("PROTEIN.fasta", aln.filetype="PHYLIP_PARS",
#                      job.name="muscleWORKFLOW1")
# myJobW2MaP <- Mafft("PROTEIN.fasta", type="PROTEIN", job.name="mafftWORKFLOW2")
# myJobW3CWD <- ClustalW("DNA.fasta", job.name="clustalwWORKFLOW3")
# myJobW4MuD <- Muscle("DNA.fasta", aln.filetype="PHYLIP_INT",
#                      job.name="muscleWORKFLOW4")

### Once all four are finished move on ###
# Wait(myJobW1MuP[[1]], minWait, maxWait)
# Wait(myJobW2MaP[[1]], minWait, maxWait)
# Wait(myJobW3CWD[[1]], minWait, maxWait)
# Wait(myJobW4MuD[[1]], minWait, maxWait)

### Now run the tree building applications ###
# myJobW1PPP <- PHYLIP_Pars("phylip_pars.aln", file.path=paste("analyses/",
#                           myJobW1MuP[[2]], sep=""), type="PROTEIN",
#                           job.name="phylipWORKFLOW1")
# myJobW2FaP <- Fasttree("mafft.fa", type="PROTEIN", file.path=paste("analyses/",
#                        myJobW2MaP[[2]], sep=""), job.name="fasttreeWORKFLOW2")
# myJobW3FaD <- Fasttree("clustalw2.fa", file.path=paste("analyses/",
#                        myJobW3CWD[[2]], sep=""), job.name="fasttreeWORKFLOW3")
# myJobW4RD <- RAxML("phylip_interleaved.aln", file.path=paste("analyses/",
#                    myJobW4MuD[[2]], sep=""), job.name="raxmlWORKFLOW4")

### Once all four are finished move on ###
# Wait(myJobW1PPP[[1]], minWait, maxWait)
# Wait(myJobW2FaP[[1]], minWait, maxWait)
# Wait(myJobW3FaD[[1]], minWait, maxWait)
# Wait(myJobW4RD[[1]], minWait, maxWait)

### Retrieve the jobs ###
# RetrieveJob(myJobW1PPP[[1]], c("outtree.nwk"))
# RetrieveJob(myJobW2FaP[[1]], c("fasttree.nwk"))
# RetrieveJob(myJobW3FaD[[1]], c("fasttree.nwk"))
# RetrieveJob(myJobW4RD[[1]], c("RAxML_bestTree.nwk"))

### Read the tree in ... ###
# read.tree(paste(getwd(), myJobW1PPP[[2]], "outtree.nwk", sep="/")) -> Tree1
# read.tree(paste(getwd(), myJobW2FaP[[2]], "fasttree.nwk", sep="/")) -> Tree2
# read.tree(paste(getwd(), myJobW3FaD[[2]], "fasttree.nwk", sep="/")) -> Tree3
# read.tree(paste(getwd(), myJobW4RD[[2]], "RAxML_bestTree.nwk", sep="/")) -> Tree4

### Plot . . . ###
# plot(Tree1)
# plot(Tree2)
# plot(Tree3)
# plot(Tree4)