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Perl command error

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# 8  
Old 11-21-2014
Well... Do you have perl installed? Where is it installed? Is it in PATH?
# 9  
Old 11-21-2014
I have perl installed here:
Code:
 C:\cygwin\bin\perl.exe

So in the VB do I need to change the
Code:
 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

to

Code:
 Set plink_object = WshShell.Run("C:\cygwin\bin\perl.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

Thank you Smilie.
# 10  
Old 11-21-2014
Yes, if it is a perl script. You run shell code using shell; you run perl code using perl.
# 11  
Old 11-22-2014
Wont that cause the bash not to run? Do I need to include both in the VB??

Code:
 Set plink_object = WshShell.Run("C:\cygwin\bin\mintty.exe C:\cygwin\bin\perl.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)

Thank you Smilie.
# 12  
Old 11-23-2014
What bash?
# 13  
Old 11-24-2014
If I run the script from the command line using:
Code:
 bash ~/windows_annovar.pl

the menu options work but the perl commands do no run.

If I use 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\perl.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

The cygwin terminal opens and closes right away.

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

The menu runs
Code:
 
Welcome to annovar, please make a selection
==================================
　
1 Match patient
2 Sanger analysis
3 Batch analysis
4 Individual analysis
5 Supplemental analysis
6 Exit
　
==================================
Your choice: 1
　
DEBUG INFO: VALUE OF $id: , VALUE OF $panel:
What is the id of the patient to be matched : H64548
What panel: Marfan20

, but the perl commands do not.

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

There seems to be something that the VB needs in order to make both the menu shell and perl work or is there a better way? Thank you Smilie.
# 14  
Old 11-24-2014
Quote:
Originally Posted by cmccabe
If I run the script from the command line using:
Code:
 bash ~/windows_annovar.pl

the menu options work but the perl commands do no run.
Then the code you have been showing is not the code you have been running.

Add Perl to your PATH or use an absolute path.
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