Subprocess.call or Subprocess.Popen cannot use executables that are in PATH (Linux/Windows)

Question

I'm writing a programme that needs to run on both Linux and Windows and use executables (with parameters) that exist in the path. (Assumed)

Currently I'm having trouble running executables in windows using Subprocess.Call and Subprocess.Popen.

For a code like this, in windows 8

def makeBlastDB(inFile, inputType, dbType, title, outDir):
    strProg = 'makeblastdb'
    strInput = '-in ' + inFile
    strInputType = '-input_type ' + inputType
    strDBType = '-dbtype ' + dbType
    strTitle = '-title ' + title
    strOut = '-out ' + os.path.join(os.sep, outDir, title)
    cmd = [strProg, strInput, strInputType, strDBType, strTitle, strOut]
    result = Popen(cmd, shell=True)

I get the error message in console

'makeblastdb' is not recognized as an internal or external command,
operable program or batch file.

Even though I can run the same command using cmd.exe I get the same response with shell=False.

Any ideas on how I can run the command assuming that the executable is in PATH environment variable? Thanks

Answer 1

You can control the environment variables available in the spawned subprocess by passing a mapping with the env keyword argument. E.g.

proc = subprocess.Popen(args, env={'PATH': '/some/path'})

Or to inherit PATH from the system environment variable, without necessarily chucking in everything else from the system environment:

proc = subprocess.Popen(args, env={'PATH': os.getenv('PATH')})

It might be easier/simpler just to use an absolute path, though.