update sh file using VBA before perl script is run - vba

Question

I have a VBA that creates a new directory folder and creates a new text file in that directory. I am trying to run a perl script from the VBA and have created a batch file that gets called from the VBA. That bat file uses a shell file to run a script. The directory in the script is dynamic and changes each time based on user input. My question is can the .sh file be updated before it is run? I apologize for the long post, just wanted to be complete. Thank you :).
VBA
Private Sub CommandButton3_Click()
Dim MyBarCode As String ' Enter Barcode
Dim MyScan As String ' Enter ScanDate
Dim MyDirectory As String
MyBarCode = Application.InputBox("Please enter the barcode", "Bar Code", Type:=2)
If MyBarCode = "False" Then Exit Sub 'user canceled
Do
MyScan = Application.InputBox("Please enter scan date", "Scan Date", Date, Type:=2)
If MyScan = "False" Then Exit Sub 'user canceled
If IsDate(MyScan) Then Exit Do
MsgBox "Please enter a valid date format. ", vbExclamation, "Invalid Date Entry"
Loop
Range("B20").Value = MyBarCode
Range("B21").Value = CDate(MyScan)
MyDirectory = "N:\1_DATA\MicroArray\NexusData\" & MyBarCode & "_" & Format(CDate(MyScan), "m-d-yyyy") & "\"
' Create nexus directory and folder
If Dir(MyDirectory, vbDirectory) = "" Then MkDir MyDirectory
If MsgBox("The project file has been created. " & _
"Do you want to create a template for analysis now?", _
vbQuestion + vbYesNo) = vbYes Then
'Write to text file
Open MyDirectory & "sample_descriptor.txt" For Output As #1
Print #1, "Experiment Sample" & vbTab & "Control Sample" & vbTab & "Display Name" & vbTab & "Gender" & vbTab & "Control Gender" & vbTab & "SpikeIn Location"
Print #1, MyBarCode & "_532Block1.txt" & vbTab & MyBarCode & "_635Block1.txt" & vbTab & ActiveSheet.Range("B8").Value & " " & ActiveSheet.Range("B9").Value & vbTab & ActiveSheet.Range("B10").Value & vbTab & ActiveSheet.Range("B5").Value & vbTab & ActiveSheet.Range("B11").Value & vbTab & ActiveSheet.Range("B12").Value
Print #1, MyBarCode & "_532Block2.txt" & vbTab & MyBarCode & "_635Block2.txt" & vbTab & ActiveSheet.Range("C8").Value & " " & ActiveSheet.Range("C9").Value & vbTab & ActiveSheet.Range("C10").Value & vbTab & ActiveSheet.Range("C5").Value & vbTab & ActiveSheet.Range("C11").Value & vbTab & ActiveSheet.Range("C12").Value
Print #1, MyBarCode & "_532Block3.txt" & vbTab & MyBarCode & "_635Block3.txt" & vbTab & ActiveSheet.Range("D8").Value & " " & ActiveSheet.Range("D9").Value & vbTab & ActiveSheet.Range("D10").Value & vbTab & ActiveSheet.Range("D5").Value & vbTab & ActiveSheet.Range("D11").Value & vbTab & ActiveSheet.Range("D12").Value
Print #1, MyBarCode & "_532Block4.txt" & vbTab & MyBarCode & "_635Block4.txt" & vbTab & ActiveSheet.Range("E8").Value & " " & ActiveSheet.Range("E9").Value & vbTab & ActiveSheet.Range("E10").Value & vbTab & ActiveSheet.Range("E5").Value & vbTab & ActiveSheet.Range("E11").Value & vbTab & ActiveSheet.Range("E12").Value
Close #1
'Run ImaGene
If MsgBox("Please run the ImaGene analysis. " & _
"and click yes after it completes to verify the spike-ins.", _
vbQuestion + vbYesNo) = vbYes Then
**'Update folder structure and call .bat
Dim PathCrnt As String
Dim FN As Long
FN = FreeFile 'FreeFile gets an available file number'
Open "C:\cygwin\home\cmccabe\Run_probes.sh" For Output As FN
PathCrnt = ActiveWorkbook.Path
*system.diagnostics.process.Start ("C:\Users\cmccabe\Desktop\NxClinical.bat") & PathCrnt*
Close FN
End If**
End Sub
Else
MsgBox "Nothing has been done. ", vbExclamation, "Goodbye!"
End If
Application.DisplayAlerts = False
Application.Quit
End Sub
Bat with that calls perl script:
C:\cygwin\bin\bash --login -i ./Run_probes.sh
Run_probes.sh
perl "C:\cygwin\home\cmccabe\get_imagene_spikein_probe_values.pl" "N:\1_DATA\MicroArray\NexusData\*257168310045_8-18-2015*" "ImaGene EmArray- Template.txt" < test_probes8.txt > "N:\1_DATA\MicroArray\NexusData\*257168310045_8-18-2015*\output.txt"

Answer 1

Nice post! Very detailed. :)
Certainly the Perl file can be updated before it is run. Just write the update path into the file like you write the data into sample_descriptor.txt. eg:
Dim FN as Long
FN = FreeFile 'FreeFile gets an available file number'
Open PathToShFile For Output As FN
Print FN, "perl " & chr(34) & PathCrnt & _
& chr(34) & "\get_imagene_spikein_probe_values.pl" & chr(34) & _
& chr(34) & "N:\1_DATA\MicroArray\NexusData\*257168310045_8-18-2015*" & _
chr(34) & " " & chr(34) & _
" ImaGene EmArray- Template.txt" & chr(34) & _
" < test_probes8.txt > " & chr(34) & _
"N:\1_DATA\MicroArray\NexusData\*257168310045_8-18-2015*\output.txt" & chr(34)
Close FN
I'm not sure I got all the " marks replaced with chr(34) correctly so make sure to echo out that string before trying to execute any code. You might also make it more readable (and configurable) by using variables to store paths. eg:
strNPath = "N:\1_DATA\MicroArray\NexusData\*257168310045_8-18-2015*\"