Problem configuering clustalW2 on windows

[Bara'a Al-Hammad]

Hello ...

How can I configure clustalW2 on windows , so I can use it via command line and biopython scripts ?

I tried to use it from within cmd but it gives me this :

'clustalW2' is not recognized as an internal or external , operable program or batch file .

Any help would be highly appreciated .

[GenoMax]

Sounds like you need to provide full path to where clustelw2 executable is located or modify your PATH so that directory is included.

[maubp]

The simplest answer is rather than "clustalw" or "clustalw2", give the full path to the binary. This is covered explicitly in the Biopython Tutorial, http://biopython.org/DIST/docs/tutorial/Tutorial.html e.g.

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = r"C:\Program Files\new clustal\clustalw2.exe"
clustalw_cline = ClustalwCommandline(clustalw_exe, infile="opuntia.fasta")
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
stdout, stderr = clustalw_cline()

Alternatively, you could try editing the $PATH environment variable (which is how this is normally solved on Linux).

[GenoMax]

To edit PATH variable in windows: http://superuser.com/questions/29794...h-in-windows-7

[Bara'a Al-Hammad]

Many thanks for your replies : GenoMax and Peter , it really helped a lot .

But now I'm facing another problem

I tried to do a very simple alignment task just to test the program , and it gave me this :



How can I deal with this ?

[GenoMax]

Test.fasta is not available in c:\Users\A-Hammad directory and the program can't open it. Provide full path instead.

[Bara'a Al-Hammad]

The simplest answer is rather than "clustalw" or "clustalw2", give the full path to the binary. This is covered explicitly in the Biopython Tutorial, http://biopython.org/DIST/docs/tutorial/Tutorial.html e.g.

import os
from Bio.Align.Applications import ClustalwCommandline
clustalw_exe = r"C:\Program Files\new clustal\clustalw2.exe"
clustalw_cline = ClustalwCommandline(clustalw_exe, infile="opuntia.fasta")
assert os.path.isfile(clustalw_exe), "Clustal W executable missing"
stdout, stderr = clustalw_cline()

Alternatively, you could try editing the $PATH environment variable (which is how this is normally solved on Linux).

To edit PATH variable in windows: http://superuser.com/questions/29794...h-in-windows-7

Can't thank you enough : Peter and GenoMax , I'm so grateful for your help .

I already knew that I should add some environmental variable to fix this , but it's really weird how it didn't work with me until you guys pointed out to the solution

That's really confusing ... does the variable name has any effect on configuring things correctly ??

[maubp]

Yes, $PATH is a special environment variable used for finding programs by name. If you try to run clustalw, or muscle, or ... then the operating system will look in all the folders listed in the $PATH setting.

[Bara'a Al-Hammad]

Thank you Peter for clarifying this