I am trying to call a perl script in R using the system command
This is what I tried:
system("perl R/BEMSER.pl -f R/fasta.txt -m R/matrix.txt -o R/result.txt -tu 100 -tl -100 -c", intern=F)
I get the following error message:
Warning message:
In system("perl R/BEMSER.pl -f R/fasta.txt -m R/matrix.txt -o R/result.txt -tu 100 -tl -100 -c", :
perl not found
The command inside the system call works in the command line (giving parameters to the perl script, the files perl should use are in a special folder called "R"), perl is of course installed.
What can I do to call the perl script from R?
Related
I am trying to run a command similar to
> system("cat <(echo $PATH)")
which fails when run from within R or Rstudio with the following error message:
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `cat <(echo $PATH)'
However, if I run this on the command line it works fine:
$ cat <(echo $PATH)
[...]/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
I checked that the shell I am using is bash using system("echo $SHELL"). Can anyone help me solving this?
This syntax works in bash but not sh. The $SHELL environment variable doesn't necessarily mean that is the shell being used. echo $0 will show your shell.
system("echo $0")
#> sh
You could force bash to be used like this
system("bash -c 'cat <(echo $PATH)'")
#> /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin
I need to issue unix commands from an R session. I'm on Windows R2 2012 server using RStudio 1.1.383 and R 3.4.3.
The shell() function looks to be the right one for me but when I specify the path to my bash shell (from Git for Windows install) the command fails with error code 127.
shell_path <- "C:\\Program Files\\Git\\git-bash.exe"
shell("ls -a", shell = shell_path)
## running command 'C:\Program Files\Git\git-bash.exe /c ls -a' had status 127'ls -a' execution failed with error code 127
Pretty sure my shell path is correct:
What am I doing wrong?
EDIT: for clarity I would like to pass any number of UNIX commands, I am just using ls -a for an example.
EDIT:
After some playing about 2018-03-09:
shell(cmd = "ls -a", shell = '"C:/Program Files/Git/bin/bash.exe"', intern = TRUE, flag = "-c")
The correct location of my bash.exe was at .../bin/bash.exe. This uses shell with intern = TRUE to return the output as an R object. Note the use of single quote marks around the shell path.
EDIT: 2018-03-09 21:40:46 UT
In RStudio we can also call bash using knitr and setting chunk options:
library(knitr)
```{bash my_bash_chunk, engine.path="C:\\Program Files\\Git\\bin\\bash.exe"}
# Using a call to unix shell
ls -a
```
Two things stand out here. Bash will return exit code 127 if a command is not found; you should try running the fully qualified command name.
I also see that your shell is being run with a /c flag. According to the documentation, the flag argument specifies "the switch to run a command under the shell" and it defaults to /c, but "if the shell is bash or tcsh or sh the default is changed to '-c'." Obviously this isn't happening for git-bash.exe.
Try these changes out:
shell_path <- "C:\\Program Files\\Git\\git-bash.exe"
shell("/bin/ls -a", shell = shell_path, flag = "-c")
Not on Windows, so can't be sure this will work.
Perhaps you need to use shQuote?
shell( paste("ls -a ", shQuote( shell_path) ) )
(Untested. I'm not on Windows. But do read ?shQuote))
If you just want to do ls -a, you can use the below commands:
shell("'ls -a'", shell="C:\\Git\\bin\\sh.exe")
#or
shell('C:\\Git\\bin\\sh.exe -c "ls -a"')
Let us know if the space in "Program Files" is causing problems.
And if you require login before you can call your command,
shell('C:\\Git\\bin\\sh.exe --login -c "ls -a"')
But if you are looking at performing git commands from R, the git2r by ropensci might suit your needs.
I'm trying to run a SLURM sbatch command with various parameters that I can read in an R script. When using PBS system, I used to write qsub -v param1=x,param2=y (+ other system parameters like the memory requirements etc and the script name to be read by PBS) and then in the R script read it with x = Sys.getenv(‘param1’).
Now I tried
sbatch run.sh --export=basePath=‘a’
With run.sh:
#!/bin/bash
cd $SLURM_SUBMIT_DIR
echo $PWD
module load R/common/3.3.3
R CMD BATCH --quiet --no-restore --no-save runDo.R output.txt
And runDo.R:
base.path = Sys.getenv('basePath')
print(base.path)
The script is running but the argument value is not assigned to base.path variable (it prints an empty string).
The export parameter has to be passed to sbatch not to the run.sh script.
It should be like this:
sbatch --export=basePath=‘a’ run.sh
please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. :
args <- commandArgs(TRUE)
TUMOR <- args[1]
GERMLINE <- args[2]
CHR <- args[3]
when I submit the R script to a PBS HPC scheduler, I do the following (below), but ... I am getting an error message.
(I am not posting the error message, because the R script I wrote works fine when it is run from a regular terminal ..)
Please may I ask, how do you usually submit the R scripts with command line arguments to PBS HPC schedulers ?
qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa#gmail.com \
-v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \
-e script.efile.chr22 \
-o script.ofile.chr22 \
script.R
I want to write an R script that will automatically send ESRI shapefiles into PostgreSQL using the shp2pgsql option in Bash.
# in Bash
shp2pgsql -I -s Port Shapefile schema.table | psql DB
# in R
Command<-c("-I","-s",Port,"shapefile","schema.table","|","psql","DB")
system2("shp2pgsql",Command,wait=FALSE)
/bin/sh: shp2pgsql: command not found
/bin/sh: psql: command not found
# Alternative in R using system
system("shp2pgsql -I -s 4326 shapefile schema.table | psql DB")
/bin/sh: shp2pgsql: command not found
/bin/sh: psql: command not found
*I understand there are other ways to achieve this result, and would appreciate answers in that regard. However, I am particularly interested in why the system2 method does not work.
Need to change to the path within R
# Find the correct directory
# Importantly, you do not want "locate psql".
# You want the directory psql is in, i.e., bin, not the full path to psql
Directory<-system("locate bin | grep /Applications/Postgres.app",inter=TRUE)[[1]]
# Create a command to redirect the path
Export<-paste("export PATH=",Directory,":$PATH",sep="")
# Create a command listing your shp2psql command
Command<-"shp2pgsql -I -s 4326 shapefile schema.table | psql DB"
# Join them using && to ensure that Export finishes before executing command
FinalCommand<-paste(Export,"&&",Command,sep=" ")
# Export it to your system
system(FinalCommand)