[Biopython] [BioPython]blastall produces a black console screen with biopython 1.49 and up
Stefanie Lück
lueck at ipk-gatersleben.de
Wed Apr 22 08:15:14 UTC 2009
Hi!
Sorry I mixed up things. It's should be windows (as in your setup.py) and not console to get no black screen!
Sorry again, I think I need holidays ;-)
Stefanie
----- Original Message -----
From: Joaquin Abian Monux
To: lueck at ipk-gatersleben.de ; biopython at maubp.freeserve.co.uk ; biopython at lists.open-bio.org
Sent: Tuesday, April 21, 2009 7:15 PM
Subject: RE: [BioPython]blastall produces a black console screen with biopython 1.49 and up
Hi Stefanie,
It is a normal, minimal setup.py for windows and single file executables:
# exWx/setup.py
from distutils.core import setup
import py2exe
setup(
windows=[
{'script': "blast_main_205.pyw",
'icon_resources':[(0,'blast.ico')]
}
],
options={
'py2exe': {
#'packages' : [],
#'includes': [],
'excludes': [
'Tkconstants','Tkinter', 'tcl'
],
'ignores': ['wxmsw26uh_vc.dll'],
'dll_excludes': ['libgdk_pixbuf-2.0-0.dll',
'libgdk-win32-2.0-0.dll',
'libgobject-2.0-0.dll'
],
'compressed': 1,
'optimize':2,
'bundle_files': 1
}
},
zipfile = None,
data_files= [
]
)
I think I understand the logic of your question. I will try with 'console' and let you know what happens. Here at work I have 1.48 installed and 1.50 at home.
Currently, with biopython 1.50, I can produce py2exe single file executables of GUI programs based on wxpython that work perfectly after:
a) I set console=True in the subprocess call in _invoke_blast (NCBIStandalone.py). Otherwise I have the Blast.exe console popping when I make a search.
b) I modify a line in the addRule function in spark.py: rules = doc.split() ---to--> rules = doc.split() if doc else []. Otherwise the executable is produced but gives an exception when ran saying that can not split 'None'.
Best regards
Joaquin
> From: lueck at ipk-gatersleben.de
> To: biopython at maubp.freeserve.co.uk; gatoygata at hotmail.com; biopython at lists.open-bio.org
> Subject: Re: [BioPython]blastall produces a black console screen with biopython 1.49 and up
> Date: Mon, 20 Apr 2009 13:07:20 +0200
>
> Hi!
>
> How does your py2exe setup.py file looks?
>
> from distutils.core import setup
> import py2exe
>
> #python setup.py py2exe
>
> setup(
> windows = [
> {
> "script": "nb_psst.py", ### Main Python
> script
> "icon_resources": [(0, "Icon.ico")] ### Icon to embed into
> the PE file.
> }
> ],
> )
>
> If you use console instead of windows in setup() will the black screen
> dissapear?
>
> Kind regards
> Stefanie
>
>
> ----- Original Message -----
> From: "Peter" <biopython at maubp.freeserve.co.uk>
> To: "Joaquin Abian Monux" <gatoygata at hotmail.com>; "BioPython Mailing List"
> <biopython at lists.open-bio.org>
> Sent: Friday, April 17, 2009 5:38 PM
> Subject: Re: [BioPython]blastall produces a black console screen with
> biopython 1.49 and up
>
>
> On Fri, Apr 17, 2009 at 4:24 PM, Joaquin Abian Monux
> <gatoygata at hotmail.com> wrote:
> > Dear Peter,
> >
> > Thanks, I fixed it. I'm not sure how.
> >
> > In:
> >
> > blast_process = subprocess.Popen(cmd_string,
> > stdout=subprocess.PIPE,
> > stderr=subprocess.PIPE,
> > stdin=subprocess.PIPE,
> > shell= (sys.platform!="win32"))
> >
> > (sys.platform!="win32") is False for my winXP computer. But if I set the
> > parameter shell=True, then the problem disappears, either in the py2exe
> > executables and in the scripts. Everything works perfect as usual.
> >
> > if shell=True in windows the shell used is the one set in COMSPEC. In my
> > case it is the normal windows shell (cmd.exe). If shell=False I am not
> > sure
> > what happens in windows. Obviously no cmd shell should be
> > expected...still,
> > blast.exe opens his.
> > ...
> > Done! (Although it would be nice someone could explain why the 'shell'
> > parameter must be 'True' for the program to behave properly)...
>
> >From memory, with subprocess using the shell argument in this way was
> deliberate on to get things to work cross platform. I looks like when
> running from the command line you need the *opposite* shell setting to
> running from py2exe.
>
> Could you put together a trivial python GUI application that calls
> BLAST that we could use for testing?
>
> Peter
>
> _______________________________________________
> Biopython mailing list - Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
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