generateBashScript: Generate a bash script
In fmichonneau/rsowh: rsowh - an R interface for the SO-WH test

Description Usage Arguments Details Value Author(s)

This function generates a bash script that runs RAxML on each of the replicated dataset.

1
2
3

generateBashScript(path, output, partfile, model, prefix, tree, seed,
  raxmlCmd = "raxmlHPC-PTHREADS-SSE3", raxmlArg = "-T7",
  overwrite = FALSE)

`path`	character string indicating the path (i.e., directory) where the simulated datasets on which to run the likelihood searches are stored.
`output`	character string indicating the file name (and path if needed) of where the script should be written.
`partfile`	character string indicating the name of the partition file to be used by RAxML during the likelihood estimations on the simulated data sets (WARNING: this is NOT the same as the partition file you might have used in your original anlysis, instead use the path for the file that was generated by `finalizeAlignments`).
`model`	character string indicating the model of molecular evolution to be used during the likelihood estimation on the replicated datasets (should be the same as the one used for the original analyses).
`prefix`	character string indicating the prefix used to name the individual RAxML runs, for instance if `prefix="best"`, the RAxML run on the first replicated dataset will be named: `RAxML_info.best-rep001`.
`tree`	If `NULL` or missing, RAxML will look for the ‘best’ tree (using the ‘`-f d`’ RAxML algorithm), otherwise a character string indicating the file name of a tree to be used as a constraint during the likelihood search (using the ‘`-f d -g`’ RAxML algorithm).
`seed`	character string indicating the seed to be used to initiate the likelihood search in RAxML. If missing a 7-digit random seed is generated.
`raxmlCmd`	character string used to call RAxML. Adjust it depending on your installation, and the flavor of RAxML you want to use, (default is “raxmlHPC-PTHREADS-SSE3”).
`raxmlArg`	character string for additional arguments to be passed to RAxML (default “-T7”)
`overwrite`	What to do when a file with the same name as the one specified by `output` already exists? if `TRUE` it will be overwritten, otherwise an error will be thrown (default `FALSE`).

For now, the bash script generated by this function is not very elegant (to say the least), but it gets the job done.

If you want to use this function by yourself, the recommended usage is to call it from the directory above where your alignments are stored.

The seed provided or generated is used in all the calls.

TRUE, but really used for its side effect of generating a bash script that contains the appropriate command to run a likelihood search on each of the replicate dataset.

Francois Michonneau

fmichonneau/rsowh documentation built on May 16, 2019, 1:47 p.m.