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raeslab / omixer-rpm

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.
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Unable to run omixer-rpm #6

Closed julianneyang closed 2 years ago

julianneyang commented 2 years ago

Hi! I've installed the latest version of omixer (0.3.2) as well as have tried all previous versions using the tar.gz files. I consistently run into this error (pasted exactly as is)

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/tmp/RtmpivXqY9/filec3e1daf500e/modules.tsv': No such file or directory

Any ideas on what this might be? Thanks in advance!

julianneyang commented 2 years ago

I found the problematic line. The (non-robust) fix is to open rpm.R and manually change this line 

out.dir <- tempfile()

to 

out.dir <-out.dir <- paste(getwd(),sep="","/outdir")

then rerun rpm(), then rerun the command using rpm.