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Perl command error

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# 1  
Old 11-20-2014
Perl command error
In the attached file I get this error. Thank you Smilie.

Code:
 C:\cygwin\home\cmccabe\windows_annovar.sh: line 117: perl: command not found

windows_annovar.sh (5.2 KB) 
# 2  
Old 11-20-2014
You can't use a shebang such as "#!/bin/bash" in Windows. It just doesn't work that way. you need to look at how to write perl code for windows. You need to run perl from a .bat file that calls the perl executable directly and passes in the perl script as an argument to the perl executable.
# 3  
Old 11-21-2014
Code:
String found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 16, near "case "$menu_choice""
        (Do you need to predeclare case?)
Number found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 17, near "1"
        (Missing semicolon on previous line?)
Bareword found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 17, near ") match"
        (Missing operator before match?)
Bareword found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 18, near ") sanger"
        (Missing operator before sanger?)
Bareword found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 19, near ") batch"
        (Missing operator before batch?)
Bareword found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 20, near ") individual"
        (Missing operator before individual?)
Bareword found where operator expected at C:\cygwin\home\cmccabe\windows_annovar.sh line 21, near ") supplemental"
        (Missing operator before supplemental?)
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 3, near ") {"
Missing comma after first argument to read function at C:\cygwin\home\cmccabe\windows_annovar.sh line 16, near "case "$menu_choice""
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 16, near "case "$menu_choice""
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 18, near "2) "
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 19, near "3) "
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 20, near "4) "
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 21, near "5) "
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 22, near "6) "
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 23, near "*) printf"
syntax error at C:\cygwin\home\cmccabe\windows_annovar.sh line 25, near "}"
C:\cygwin\home\cmccabe\windows_annovar.sh has too many errors.

I am not sure where to go. Thank you Smilie.
windows_annovar.sh (5.2 KB) 
# 4  
Old 11-21-2014
You have to run it with perl commandname. Windows doesn't know or care what the #! line is.

Since it is not a bourne shell file, you shouldn't name it sh either. .pl would be more traditional for perl scripts.
# 5  
Old 11-21-2014
I am trying to use VB in excel to call and execute the .sh file:

VB
Code:
 
Private Sub CommandButton1_Click()
    Dim cmd As String
    Dim ret As Double
    Dim WshShell As Object
    Dim plink_object As Object
    ' Run Linux Commands
    Set WshShell = CreateObject("WScript.Shell")
    On Error Resume Next
    Set plink_object = WshShell.Run("C:\cygwin\bin\mintty.exe C:\cygwin\home\cmccabe\windows_annovar.sh 66 ""50602_15:56:31_15:56:11_15:56:21;50602_15:57:07_15:56:47_15:56:57""", 1)
    On Error GoTo 0
End Sub

As of know it errors on the perl commands:
Code:
 C:\cygwin\home\cmccabe\windows_annovar.sh: line 117: perl: command not found

As a bash it runs fine as is but windows doesent seem to like it. I am not familiar enough with windows and perl.... linux seems much nicier. Thanks Smilie.
# 6  
Old 11-21-2014
Quote:
Originally Posted by cmccabe
I am trying to use VB in excel to call and execute the .sh file
For the third time -- it is not an sh file. You should be running it in perl because it is perl and not shell.

Running it in shell instead of perl will cause the problems you have seen, because the shell does not understand the perl code when running it in shell instead of perl.

The way to run it is to use perl instead of shell, so it runs using perl, which understands perl programs.

... mintty.exe perl script.sh
# 7  
Old 11-21-2014
VB
Code:
 Private Sub CommandButton1_Click()
    Dim cmd As String
    Dim ret As Double
    Dim WshShell As Object
    Dim plink_object As Object
    ' Run Linux Commands
    Set WshShell = CreateObject("WScript.Shell")
    On Error Resume Next
    Set plink_object = WshShell.Run("C:\cygwin\bin\mintty.exe C:\cygwin\home\cmccabe\windows_annovar.pl 66 ""50602_15:56:31_15:56:11_15:56:21;50602_15:57:07_15:56:47_15:56:57""", 1)
    On Error GoTo 0
End Sub

Code:
 
C:\cygwin\home\cmccabe\windows_annovar.pl: line 36: perl: command not found

perl code:
Code:
 match() {
    printf "\n\n"
    printf "DEBUG INFO: VALUE OF \$id: %s, VALUE OF \$panel: %s\n" $id $panel
    printf "What is the id of the patient to be matched  : "; read id
    printf "What panel: "; read panel
    [ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && menu
    [ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && menu
    cd 'C:\Users\cmccabe\Desktop\annovar'
    OMR=Output_Mutation_Report
               perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf
    convert

from the perl code I removed the $( ). Thank you Smilie.
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