render_blast problem

[Kie Kyon Huang]

Hi,

I was trying to follow the HOWTO:Graphics at
http://www.bioperl.org/wiki/HOWTO:Graphics

When running the command line in cygwin

$ perl render_blast1.pl data1.txt | display -

I get the following error line,

bash: display: command not found

I also tried

$ perl render_blast1.pl data1.txt > data1.png

however, I was unable to open the data1.png file using Microsoft
Office Picture Manager or windows Photo Gallery

Thanks

Huang
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[Peter-329]

On Tue, Nov 3, 2009 at 3:14 PM, Kie Kyon Huang <kiekyon.huang@...> wrote:

> Hi,
>
> I was trying to follow the HOWTO:Graphics at
> http://www.bioperl.org/wiki/HOWTO:Graphics
>
> When running the command line in cygwin
>
> $ perl render_blast1.pl data1.txt | display -
>
> I get the following error line,
>
> bash: display: command not found

That makes sense on Windows, since display is a Unix
command line tool.

> I also tried
>
> $ perl render_blast1.pl data1.txt > data1.png

Based on the wiki, I think that ought to have worked.

> however, I was unable to open the data1.png file using Microsoft
> Office Picture Manager or windows Photo Gallery

Did you do this step?:
>> Important!  If you are on a Windows platform, you need to put
>> STDOUT into binary mode so that the PNG file does not go
>> through Window's carriage return/linefeed transformations.
>> Before the final print statement, put the statement
>> binmode(STDOUT). This advice also applies to certain older
>> versions of RedHat, which ship with a patched (and possibly
>> broken) version of Perl.

(BioPerl devs - couldn't that be added to the default
render_blast1.pl script with an if statement checking for
Windows?)

Peter
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[Peter-329]

Mailing list CC'd - solved :)

On Tue, Nov 3, 2009 at 3:55 PM, Kie Kyon Huang <kiekyon.huang@...> wrote:
>
> ok, that fix it
> i forget sometimes what platform am i on.
> thanks

Great.

Peter
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[Chris Fields-5]

On Nov 3, 2009, at 9:45 AM, Peter wrote:

> ...
> Did you do this step?:
>>> Important!  If you are on a Windows platform, you need to put
>>> STDOUT into binary mode so that the PNG file does not go
>>> through Window's carriage return/linefeed transformations.
>>> Before the final print statement, put the statement
>>> binmode(STDOUT). This advice also applies to certain older
>>> versions of RedHat, which ship with a patched (and possibly
>>> broken) version of Perl.
>
> (BioPerl devs - couldn't that be added to the default
> render_blast1.pl script with an if statement checking for
> Windows?)
>
> Peter

Yes, that should be added.  I'll work on it.

chris
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