error on Rstudio

[AnneJRomero]

Hi,

I have followed the installation steps on here and am trying to get this to work on RStudio but I get the following errors when I try and run the test.fasta.

test <- readDNAStringSet("test.fasta", format = "fasta")

itsx(
test,
out_root = tempfile("itsx"),
taxon = "fungi",
e_value = 1e-05,
s_value = 0,
n_value = 2,
selection_priority = c("score", "sum", "domains", "eval"),
search_eval = 0.05,
#search_score = NULL,
allow_single_domain = c(1e-09, 0),
allow_reorder = FALSE,
complement = TRUE,
#cpu = 1,
#multi_thread = cpu > 1,
heuristics = FALSE,
nhmmer = FALSE,
summary = TRUE,
graphical = TRUE,
fasta = TRUE,
preserve = FALSE,
save_regions = c("ITS1", "ITS2", "5.8S"),
anchor = 0,
require_anchor = 0,
only_full = FALSE,
partial = 0,
concat = FALSE,
minlen = 0,
positions = TRUE,
table = FALSE,
detailed_results = FALSE,
not_found = TRUE,
truncate = TRUE,
silent = FALSE,
graph_scale = 0,
save_raw = FALSE,
read_function = FALSE
)

Error in glue_data(.x = NULL, ..., .sep = .sep, .envir = .envir, .open = .open, :
Expecting '}'

I would appriciate your help. Thank you.

[brendanf]

I believe I fixed this now with f8950c8. Can you please test with the latest github version (i.e., remotes::install_github("brendanf/rITSx"))

[AnneJRomero]

Hi, thank you for your quick reply. I got a new error below

Error in itsx(test, out_root = tempfile("itsx"), taxon = "fungi", e_value = 1e-05, :
ITSx failed with return code 127.

[brendanf]

That sounds like a problem finding the ITSx script. What operating system are you using and how did you install ITSx?

[AnneJRomero]

I have Microsoft windows, and using the Rstudio Desktop.

[brendanf]

Did you download ITSx and install it?

[AnneJRomero]

I have downloaded it (with the files below) but I'm not sure how to install it?

[brendanf]

I realize now that it is probably difficult to use ITSx (and therefore rITSx) on Windows, because it uses Hmmer internally, and according to the Hmmer documentation, it cannot be installed directly in Windows. They mention using the Linux subsystem for Windows, but I am unfortunately not qualified to give advice about how to do that in practice, or how to access it from R running in Windows (alternatively, how to run R studio inside the Linux subsystem). Sorry!

As an alternative, I think you can run ITSx online in PlutoF, and that PipeCraft can run it in Windows using Docker containers.

[AnneJRomero]

Thank you so much for your help :)