BioPerl Installation Problem...Please help me...

[Prem-10]

Hello sir,



I am Prem Krishnan, doing MSc. in Computational Biology.

I am interested in Perl language and now I am started studying Bioperl.

But I met with some problems during the installation.



Details are given below,



Using operating system      :-       *Windows XP 2 version*

Perl Version                      :-       *Active Perl 5.8.8.819*



I started installation using GUI method.

I followed the guidelines from the site
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows.


The steps in that link includes the following,
Installation using the Perl Package Manager GUI Installation

1) Start the Perl Package Manager GUI from the Start menu.

2) Go to Edit >> Preferences and click the Repositories tab. Add a new
repository for each of the following (note the difference based on the perl
version):

Repositories to add

*Name *

*perl 5.8 *

*perl 5.10 *

BioPerl-Regular Releases

http://bioperl.org/DIST

http://bioperl.org/DIST

BioPerl-Release Candidates

http://bioperl.org/DIST/RC

http://bioperl.org/DIST/RC

Kobes

http://theoryx5.uwinnipeg.ca/ppms

http://cpan.uwinnipeg.ca/PPMPackages/10xx/

Bribes

http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>

http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>

tcool

http://ppm.tcool.org/archives/

NA

3) Select View >> All Packages.

4) In the search box type bioperl.

5) Right click the latest version of Bioperl available and choose install.
(Note for users of previous Bioperl releases: you should not have to use the
Bundle-BioPerl package anymore.)

5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will be marked
for installation. If you see that some of them complain about needing a
command-line installation (eg. XML::SAX::ExpatXS), and you want those
particular pre-requisites, stop now (skip step 6) and see the 'Command-line
Installation' section.

6) Click the green arrow (Run marked actions) to complete the installation.



*I had completed the first ‘Three’ steps*. But when I tried to execute
the*fourth step
* I couldn’t find any *bioperl packages*.



What I can I do to make my installation successful? Please help me.

I think the information explained above is enough for you to understand my
problem.

Thanks in advance…


Prem krishnan
There can be miracles if you believe in you...
http://www.google.com/profiles/premkrishnanbv

_______________________________________________
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Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Chris Fields-5]

The PPM hasn't been updated for Windows as of yet.  I would assume if  
you use the specified version of ActivePerl it should work still, but  
only for 1.5.2.

I am working on getting a PPM working for 1.6.1 (it was supposed to be  
posted last week) but have been flooded with other work, though it  
isn't off my agenda, just pushed back on the priority list a wee bit,  
until I can get a few other things going.

chris

On Oct 5, 2009, at 3:13 AM, Prem wrote:

> Hello sir,
>
>
>
> I am Prem Krishnan, doing MSc. in Computational Biology.
>
> I am interested in Perl language and now I am started studying  
> Bioperl.
>
> But I met with some problems during the installation.
>
>
>
> Details are given below,
>
>
>
> Using operating system      :-       *Windows XP 2 version*
>
> Perl Version                      :-       *Active Perl 5.8.8.819*
>
>
>
> I started installation using GUI method.
>
> I followed the guidelines from the site
> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows.
>
>
> The steps in that link includes the following,
> Installation using the Perl Package Manager GUI Installation
>
> 1) Start the Perl Package Manager GUI from the Start menu.
>
> 2) Go to Edit >> Preferences and click the Repositories tab. Add a new
> repository for each of the following (note the difference based on  
> the perl
> version):
>
> Repositories to add
>
> *Name *
>
> *perl 5.8 *
>
> *perl 5.10 *
>
> BioPerl-Regular Releases
>
> http://bioperl.org/DIST
>
> http://bioperl.org/DIST
>
> BioPerl-Release Candidates
>
> http://bioperl.org/DIST/RC
>
> http://bioperl.org/DIST/RC
>
> Kobes
>
> http://theoryx5.uwinnipeg.ca/ppms
>
> http://cpan.uwinnipeg.ca/PPMPackages/10xx/
>
> Bribes
>
> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>
>
> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>
>
> tcool
>
> http://ppm.tcool.org/archives/
>
> NA
>
> 3) Select View >> All Packages.
>
> 4) In the search box type bioperl.
>
> 5) Right click the latest version of Bioperl available and choose  
> install.
> (Note for users of previous Bioperl releases: you should not have to  
> use the
> Bundle-BioPerl package anymore.)
>
> 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will be  
> marked
> for installation. If you see that some of them complain about  
> needing a
> command-line installation (eg. XML::SAX::ExpatXS), and you want those
> particular pre-requisites, stop now (skip step 6) and see the  
> 'Command-line
> Installation' section.
>
> 6) Click the green arrow (Run marked actions) to complete the  
> installation.
>
>
>
> *I had completed the first ‘Three’ steps*. But when I tried to execute
> the*fourth step
> * I couldn’t find any *bioperl packages*.
>
>
>
> What I can I do to make my installation successful? Please help me.
>
> I think the information explained above is enough for you to  
> understand my
> problem.
>
> Thanks in advance…
>
>
> Prem krishnan
> There can be miracles if you believe in you...
> http://www.google.com/profiles/premkrishnanbv
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Chris Fields-5]

That was a bit of a run-on.  Shows I need my coffee...

chris

On Oct 7, 2009, at 7:57 AM, Chris Fields wrote:

> The PPM hasn't been updated for Windows as of yet.  I would assume  
> if you use the specified version of ActivePerl it should work still,  
> but only for 1.5.2.
>
> I am working on getting a PPM working for 1.6.1 (it was supposed to  
> be posted last week) but have been flooded with other work, though  
> it isn't off my agenda, just pushed back on the priority list a wee  
> bit, until I can get a few other things going.
>
> chris
>
> On Oct 5, 2009, at 3:13 AM, Prem wrote:
>
>> Hello sir,
>>
>>
>>
>> I am Prem Krishnan, doing MSc. in Computational Biology.
>>
>> I am interested in Perl language and now I am started studying  
>> Bioperl.
>>
>> But I met with some problems during the installation.
>>
>>
>>
>> Details are given below,
>>
>>
>>
>> Using operating system      :-       *Windows XP 2 version*
>>
>> Perl Version                      :-       *Active Perl 5.8.8.819*
>>
>>
>>
>> I started installation using GUI method.
>>
>> I followed the guidelines from the site
>> http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows.
>>
>>
>> The steps in that link includes the following,
>> Installation using the Perl Package Manager GUI Installation
>>
>> 1) Start the Perl Package Manager GUI from the Start menu.
>>
>> 2) Go to Edit >> Preferences and click the Repositories tab. Add a  
>> new
>> repository for each of the following (note the difference based on  
>> the perl
>> version):
>>
>> Repositories to add
>>
>> *Name *
>>
>> *perl 5.8 *
>>
>> *perl 5.10 *
>>
>> BioPerl-Regular Releases
>>
>> http://bioperl.org/DIST
>>
>> http://bioperl.org/DIST
>>
>> BioPerl-Release Candidates
>>
>> http://bioperl.org/DIST/RC
>>
>> http://bioperl.org/DIST/RC
>>
>> Kobes
>>
>> http://theoryx5.uwinnipeg.ca/ppms
>>
>> http://cpan.uwinnipeg.ca/PPMPackages/10xx/
>>
>> Bribes
>>
>> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>
>>
>> http://www.Bribes.org/perl/ppm <http://www.bribes.org/perl/ppm>
>>
>> tcool
>>
>> http://ppm.tcool.org/archives/
>>
>> NA
>>
>> 3) Select View >> All Packages.
>>
>> 4) In the search box type bioperl.
>>
>> 5) Right click the latest version of Bioperl available and choose  
>> install.
>> (Note for users of previous Bioperl releases: you should not have  
>> to use the
>> Bundle-BioPerl package anymore.)
>>
>> 5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will  
>> be marked
>> for installation. If you see that some of them complain about  
>> needing a
>> command-line installation (eg. XML::SAX::ExpatXS), and you want those
>> particular pre-requisites, stop now (skip step 6) and see the  
>> 'Command-line
>> Installation' section.
>>
>> 6) Click the green arrow (Run marked actions) to complete the  
>> installation.
>>
>>
>>
>> *I had completed the first ‘Three’ steps*. But when I tried to  
>> execute
>> the*fourth step
>> * I couldn’t find any *bioperl packages*.
>>
>>
>>
>> What I can I do to make my installation successful? Please help me.
>>
>> I think the information explained above is enough for you to  
>> understand my
>> problem.
>>
>> Thanks in advance…
>>
>>
>> Prem krishnan
>> There can be miracles if you believe in you...
>> http://www.google.com/profiles/premkrishnanbv
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@...
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[Robert Buels]

Chris Fields wrote:
> That was a bit of a run-on.  Shows I need my coffee...
>
> chris

I think that would probably just make it worse.


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Bioperl-l@...
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[Chris Fields-5]

Nope, that fixed it up.  Now just too jittery to code...

chris

On Oct 7, 2009, at 1:03 PM, Robert Buels wrote:

> Chris Fields wrote:
>> That was a bit of a run-on.  Shows I need my coffee...
>> chris
>
> I think that would probably just make it worse.
>
>

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l