help!

classic Classic list List threaded Threaded
15 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

help!

Casandra-12
Hi, 

I'm trying to install Bioperl but I'm a bit lost. I know I have perl installed becaused I have already write some scripts but I'm biologist so... not pretty sure about what messages say.

My perl version:
This is perl, v5.8.8 built for darwin-thread-multi-2level
My computer:
Mac OS X Vesion 10.5.8

I was following this preliminary steps:

--------------
PRELIMINARY PREPARATION

   This is optional, but regardless of your subsequent choice of
   installation method, it will help to carry out the following steps.
   They will increase the likelyhood of installation success
   (especially of optional dependencies).

     * Upgrade CPAN:

 >perl -MCPAN -e shell
 cpan>install Bundle::CPAN
 cpan>q				

     * Install/upgrade Module::Build, and make it your preferred
       installer:

 >cpan
 cpan>install Module::Build
 cpan>o conf prefer_installer MB
 cpan>o conf commit
 cpan>q

     * Install the expat library by whatever method is
       appropriate for your system.

     * If your expat library is installed in a non-standard location,
       tell CPAN about it:

 >cpan
 cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include"
 cpan>o conf commit
--------------
And I think I did "Upgrade CPAN properly" but when I tried the next one it started asking too many things to me, and finally it stopped due to "some problems". In text file you can see the whole process.
What did I do wrong?


After solving these preliminary steps, what should I do? What exactly .tar or .whatever should I download to install?

I don't see the difference between installing it through "built.PL" or  CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC. 

* I went to Fink webpage and what I expected to see was "hello! download Bioperl simply clicking here!" but far from this, what it seems is that first I have to download some kinf of Fink-program before starting with Bioperl... is it something close to this?

I'm sorry, too many questions... But I really want to learn to use Bioperl but I have no people to ask it face to face.

Thank you so much, 

Casandra

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l

terminal.txt (3K) Download Attachment
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Scott Cain-4
hi Cassandra,

I don't have an answer for you at the moment.  It seems to me that
using local::lib is a good idea, but I've never found a good tutorial
for using it, so I haven't.  Perhaps someone else on the list can
suggest one.

The other thing I just wanted to mention as the admin that approved
your message--I came very close to deleting it from the queue without
looking at it because it is not unusual for spam messages to have
generic subjects like "help!"  (just for future reference :-)

Scott


On Tue, Feb 7, 2012 at 11:11 AM, Casandra <[hidden email]> wrote:

> Hi,
>
> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> installed becaused I have already write some scripts but I'm biologist so...
> not pretty sure about what messages say.
>
> My perl version:
> This is perl, v5.8.8 built for darwin-thread-multi-2level
> My computer:
> Mac OS X Vesion 10.5.8
>
> I was following this preliminary steps:
>
> --------------
>
> PRELIMINARY PREPARATION
>
>    This is optional, but regardless of your subsequent choice of
>    installation method, it will help to carry out the following steps.
>    They will increase the likelyhood of installation success
>    (especially of optional dependencies).
>
>      * Upgrade CPAN:
>
>  >perl -MCPAN -e shell
>  cpan>install Bundle::CPAN
>  cpan>q
>
>      * Install/upgrade Module::Build, and make it your preferred
>        installer:
>
>  >cpan
>  cpan>install Module::Build
>  cpan>o conf prefer_installer MB
>  cpan>o conf commit
>  cpan>q
>
>      * Install the expat library by whatever method is
>        appropriate for your system.
>
>      * If your expat library is installed in a non-standard location,
>        tell CPAN about it:
>
>  >cpan
>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> EXPATINCPATH=/non-standard/include"
>  cpan>o conf commit
>
> --------------
>
> And I think I did "Upgrade CPAN properly" but when I tried the next one it
> started asking too many things to me, and finally it stopped due to "some
> problems". In text file you can see the whole process.
> What did I do wrong?
>
>
> After solving these preliminary steps, what should I do? What exactly .tar
> or .whatever should I download to install?
>
> I don't see the difference between installing it through "built.PL" or
>  CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>
> * I went to Fink webpage and what I expected to see was "hello! download
> Bioperl simply clicking here!" but far from this, what it seems is that
> first I have to download some kinf of Fink-program before starting with
> Bioperl... is it something close to this?
>
> I'm sorry, too many questions... But I really want to learn to use Bioperl
> but I have no people to ask it face to face.
>
> Thank you so much,
>
> Casandra
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Fields, Christopher J
I guess one key question is where these CPAN installation instructions
come from.  They're a bit odd, and if this is from the wiki we need to
do some updating.

Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
single perl version.

https://metacpan.org/module/local::lib#The-bootstrapping-technique

In my case I use perlbrew (which is all local by default, and allows
switching between perl versions).  Highly recommend using either simple
local::lib or perlbrew in combination with cpanm.

https://metacpan.org/module/perlbrew
https://metacpan.org/module/cpanm

chris


On 02/07/2012 02:55 PM, Scott Cain wrote:

> hi Cassandra,
>
> I don't have an answer for you at the moment.  It seems to me that
> using local::lib is a good idea, but I've never found a good tutorial
> for using it, so I haven't.  Perhaps someone else on the list can
> suggest one.
>
> The other thing I just wanted to mention as the admin that approved
> your message--I came very close to deleting it from the queue without
> looking at it because it is not unusual for spam messages to have
> generic subjects like "help!"  (just for future reference :-)
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>  wrote:
>> Hi,
>>
>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>> installed becaused I have already write some scripts but I'm biologist so...
>> not pretty sure about what messages say.
>>
>> My perl version:
>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>> My computer:
>> Mac OS X Vesion 10.5.8
>>
>> I was following this preliminary steps:
>>
>> --------------
>>
>> PRELIMINARY PREPARATION
>>
>>     This is optional, but regardless of your subsequent choice of
>>     installation method, it will help to carry out the following steps.
>>     They will increase the likelyhood of installation success
>>     (especially of optional dependencies).
>>
>>       * Upgrade CPAN:
>>
>>   >perl -MCPAN -e shell
>>   cpan>install Bundle::CPAN
>>   cpan>q
>>
>>       * Install/upgrade Module::Build, and make it your preferred
>>         installer:
>>
>>   >cpan
>>   cpan>install Module::Build
>>   cpan>o conf prefer_installer MB
>>   cpan>o conf commit
>>   cpan>q
>>
>>       * Install the expat library by whatever method is
>>         appropriate for your system.
>>
>>       * If your expat library is installed in a non-standard location,
>>         tell CPAN about it:
>>
>>   >cpan
>>   cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>> EXPATINCPATH=/non-standard/include"
>>   cpan>o conf commit
>>
>> --------------
>>
>> And I think I did "Upgrade CPAN properly" but when I tried the next one it
>> started asking too many things to me, and finally it stopped due to "some
>> problems". In text file you can see the whole process.
>> What did I do wrong?
>>
>>
>> After solving these preliminary steps, what should I do? What exactly .tar
>> or .whatever should I download to install?
>>
>> I don't see the difference between installing it through "built.PL" or
>>   CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>>
>> * I went to Fink webpage and what I expected to see was "hello! download
>> Bioperl simply clicking here!" but far from this, what it seems is that
>> first I have to download some kinf of Fink-program before starting with
>> Bioperl... is it something close to this?
>>
>> I'm sorry, too many questions... But I really want to learn to use Bioperl
>> but I have no people to ask it face to face.
>>
>> Thank you so much,
>>
>> Casandra
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Scott Cain-4
Yes, but those doc don't address exactly the problem Cassandra is
having, that she wants to use local::lib, but there need to be some
prereqs installed, but they can't be because she chose to use
local::lib, and it's not installed.  That's all fine if you're not a
newbie and know how to properly install the prereqs before using the
cpan shell, but when following instructions that say "use local::lib",
I find that the instructions are completely insufficient in actually
getting the desired software installed.  Thus the need for a good
tutorial.

Scott


On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]> wrote:

> I guess one key question is where these CPAN installation instructions come
> from.  They're a bit odd, and if this is from the wiki we need to do some
> updating.
>
> Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> single perl version.
>
> https://metacpan.org/module/local::lib#The-bootstrapping-technique
>
> In my case I use perlbrew (which is all local by default, and allows
> switching between perl versions).  Highly recommend using either simple
> local::lib or perlbrew in combination with cpanm.
>
> https://metacpan.org/module/perlbrew
> https://metacpan.org/module/cpanm
>
> chris
>
>
>
> On 02/07/2012 02:55 PM, Scott Cain wrote:
>>
>> hi Cassandra,
>>
>> I don't have an answer for you at the moment.  It seems to me that
>> using local::lib is a good idea, but I've never found a good tutorial
>> for using it, so I haven't.  Perhaps someone else on the list can
>> suggest one.
>>
>> The other thing I just wanted to mention as the admin that approved
>> your message--I came very close to deleting it from the queue without
>> looking at it because it is not unusual for spam messages to have
>> generic subjects like "help!"  (just for future reference :-)
>>
>> Scott
>>
>>
>> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>  wrote:
>>>
>>> Hi,
>>>
>>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>> installed becaused I have already write some scripts but I'm biologist
>>> so...
>>> not pretty sure about what messages say.
>>>
>>> My perl version:
>>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>> My computer:
>>> Mac OS X Vesion 10.5.8
>>>
>>> I was following this preliminary steps:
>>>
>>> --------------
>>>
>>> PRELIMINARY PREPARATION
>>>
>>>    This is optional, but regardless of your subsequent choice of
>>>    installation method, it will help to carry out the following steps.
>>>    They will increase the likelyhood of installation success
>>>    (especially of optional dependencies).
>>>
>>>      * Upgrade CPAN:
>>>
>>>  >perl -MCPAN -e shell
>>>  cpan>install Bundle::CPAN
>>>  cpan>q
>>>
>>>      * Install/upgrade Module::Build, and make it your preferred
>>>        installer:
>>>
>>>  >cpan
>>>  cpan>install Module::Build
>>>  cpan>o conf prefer_installer MB
>>>  cpan>o conf commit
>>>  cpan>q
>>>
>>>      * Install the expat library by whatever method is
>>>        appropriate for your system.
>>>
>>>      * If your expat library is installed in a non-standard location,
>>>        tell CPAN about it:
>>>
>>>  >cpan
>>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>> EXPATINCPATH=/non-standard/include"
>>>  cpan>o conf commit
>>>
>>> --------------
>>>
>>> And I think I did "Upgrade CPAN properly" but when I tried the next one
>>> it
>>> started asking too many things to me, and finally it stopped due to "some
>>> problems". In text file you can see the whole process.
>>> What did I do wrong?
>>>
>>>
>>> After solving these preliminary steps, what should I do? What exactly
>>> .tar
>>> or .whatever should I download to install?
>>>
>>> I don't see the difference between installing it through "built.PL" or
>>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>> MAC.
>>>
>>> * I went to Fink webpage and what I expected to see was "hello! download
>>> Bioperl simply clicking here!" but far from this, what it seems is that
>>> first I have to download some kinf of Fink-program before starting with
>>> Bioperl... is it something close to this?
>>>
>>> I'm sorry, too many questions... But I really want to learn to use
>>> Bioperl
>>> but I have no people to ask it face to face.
>>>
>>> Thank you so much,
>>>
>>> Casandra
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Joseph Guhlin-3
In reply to this post by Casandra-12
I wonder if this would work on your system?

http://www.sysarchitects.com/bioperl

Best,
--Joseph Guhlin

On Tue, Feb 7, 2012 at 10:11 AM, Casandra <[hidden email]> wrote:

> Hi,
>
> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> installed becaused I have already write some scripts but I'm biologist
> so... not pretty sure about what messages say.
>
> My perl version:
> This is perl, v5.8.8 built for darwin-thread-multi-2level
> My computer:
> Mac OS X Vesion 10.5.8
>
> I was following this preliminary steps:
>
> --------------
>
> PRELIMINARY PREPARATION
>
>    This is optional, but regardless of your subsequent choice of
>    installation method, it will help to carry out the following steps.
>    They will increase the likelyhood of installation success
>    (especially of optional dependencies).
>
>      * Upgrade CPAN:
>
>  >perl -MCPAN -e shell
>  cpan>install Bundle::CPAN
>  cpan>q
>
>      * Install/upgrade Module::Build, and make it your preferred
>        installer:
>
>  >cpan
>  cpan>install Module::Build
>  cpan>o conf prefer_installer MB
>  cpan>o conf commit
>  cpan>q
>
>      * Install the expat library by whatever method is
>        appropriate for your system.
>
>      * If your expat library is installed in a non-standard location,
>        tell CPAN about it:
>
>  >cpan
>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib EXPATINCPATH=/non-standard/include"
>  cpan>o conf commit
>
> --------------
>
> And I think I did "Upgrade CPAN properly" but when I tried the next one it
> started asking too many things to me, and finally it stopped due to "some
> problems". In text file you can see the whole process.
> What did I do wrong?
>
>
> After solving these preliminary steps, what should I do? What exactly .tar
> or .whatever should I download to install?
>
> I don't see the difference between installing it through "built.PL" or
>  CPAN. And I don't know if I should do this or that "Fink*" stuff for MAC.
>
> * I went to Fink webpage and what I expected to see was "hello! download
> Bioperl simply clicking here!" but far from this, what it seems is that
> first I have to download some kinf of Fink-program before starting with
> Bioperl... is it something close to this?
>
> I'm sorry, too many questions... But I really want to learn to use Bioperl
> but I have no people to ask it face to face.
>
> Thank you so much,
>
> Casandra
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Fields, Christopher J
In reply to this post by Scott Cain-4
Right, I see.  However, Casandra didn't mention using local::lib, just
using CPAN in general (hence my initial question).

IIRC local::lib, if set up correctly, should take care of the
installation paths for CPAN/cpanm/etc regardless whether it's bioperl or
any other perl module.

Last I checked this didn't seem to be an issue with bioperl; I installed
Bioperl, as well as any prereqs, Bio::DB::Sam/BigWig, Moose,
DBD::SQLite, etc, on our local SGI using local::lib in a common project
space (with perl 5.10.1) w/o a problem.  If there is a problem specific
to BioPerl, we should probably try to fix it and clarify any workarounds
in the meantime.

chris

On 02/07/2012 03:12 PM, Scott Cain wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields<[hidden email]>  wrote:
>> I guess one key question is where these CPAN installation instructions come
>> from.  They're a bit odd, and if this is from the wiki we need to do some
>> updating.
>>
>> Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>> single perl version.
>>
>> https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>
>> In my case I use perlbrew (which is all local by default, and allows
>> switching between perl versions).  Highly recommend using either simple
>> local::lib or perlbrew in combination with cpanm.
>>
>> https://metacpan.org/module/perlbrew
>> https://metacpan.org/module/cpanm
>>
>> chris
>>
>>
>>
>> On 02/07/2012 02:55 PM, Scott Cain wrote:
>>>
>>> hi Cassandra,
>>>
>>> I don't have an answer for you at the moment.  It seems to me that
>>> using local::lib is a good idea, but I've never found a good tutorial
>>> for using it, so I haven't.  Perhaps someone else on the list can
>>> suggest one.
>>>
>>> The other thing I just wanted to mention as the admin that approved
>>> your message--I came very close to deleting it from the queue without
>>> looking at it because it is not unusual for spam messages to have
>>> generic subjects like "help!"  (just for future reference :-)
>>>
>>> Scott
>>>
>>>
>>> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>    wrote:
>>>>
>>>> Hi,
>>>>
>>>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>>> installed becaused I have already write some scripts but I'm biologist
>>>> so...
>>>> not pretty sure about what messages say.
>>>>
>>>> My perl version:
>>>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>>> My computer:
>>>> Mac OS X Vesion 10.5.8
>>>>
>>>> I was following this preliminary steps:
>>>>
>>>> --------------
>>>>
>>>> PRELIMINARY PREPARATION
>>>>
>>>>     This is optional, but regardless of your subsequent choice of
>>>>     installation method, it will help to carry out the following steps.
>>>>     They will increase the likelyhood of installation success
>>>>     (especially of optional dependencies).
>>>>
>>>>       * Upgrade CPAN:
>>>>
>>>>   >perl -MCPAN -e shell
>>>>   cpan>install Bundle::CPAN
>>>>   cpan>q
>>>>
>>>>       * Install/upgrade Module::Build, and make it your preferred
>>>>         installer:
>>>>
>>>>   >cpan
>>>>   cpan>install Module::Build
>>>>   cpan>o conf prefer_installer MB
>>>>   cpan>o conf commit
>>>>   cpan>q
>>>>
>>>>       * Install the expat library by whatever method is
>>>>         appropriate for your system.
>>>>
>>>>       * If your expat library is installed in a non-standard location,
>>>>         tell CPAN about it:
>>>>
>>>>   >cpan
>>>>   cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>>> EXPATINCPATH=/non-standard/include"
>>>>   cpan>o conf commit
>>>>
>>>> --------------
>>>>
>>>> And I think I did "Upgrade CPAN properly" but when I tried the next one
>>>> it
>>>> started asking too many things to me, and finally it stopped due to "some
>>>> problems". In text file you can see the whole process.
>>>> What did I do wrong?
>>>>
>>>>
>>>> After solving these preliminary steps, what should I do? What exactly
>>>> .tar
>>>> or .whatever should I download to install?
>>>>
>>>> I don't see the difference between installing it through "built.PL" or
>>>>   CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>>> MAC.
>>>>
>>>> * I went to Fink webpage and what I expected to see was "hello! download
>>>> Bioperl simply clicking here!" but far from this, what it seems is that
>>>> first I have to download some kinf of Fink-program before starting with
>>>> Bioperl... is it something close to this?
>>>>
>>>> I'm sorry, too many questions... But I really want to learn to use
>>>> Bioperl
>>>> but I have no people to ask it face to face.
>>>>
>>>> Thank you so much,
>>>>
>>>> Casandra
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Dave Messina-3
In reply to this post by Scott Cain-4
I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.

Best,
Dave



 There’s a quickie, “zero-install” way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master


    when it's done downloading, unzip it if your computer hasn’t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!












On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]> wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]>
> wrote:
> > I guess one key question is where these CPAN installation instructions
> come
> > from.  They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> >
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> >
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >
> > In my case I use perlbrew (which is all local by default, and allows
> > switching between perl versions).  Highly recommend using either simple
> > local::lib or perlbrew in combination with cpanm.
> >
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> >
> > chris
> >
> >
> >
> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >>
> >> hi Cassandra,
> >>
> >> I don't have an answer for you at the moment.  It seems to me that
> >> using local::lib is a good idea, but I've never found a good tutorial
> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> suggest one.
> >>
> >> The other thing I just wanted to mention as the admin that approved
> >> your message--I came very close to deleting it from the queue without
> >> looking at it because it is not unusual for spam messages to have
> >> generic subjects like "help!"  (just for future reference :-)
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>  wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >>> installed becaused I have already write some scripts but I'm biologist
> >>> so...
> >>> not pretty sure about what messages say.
> >>>
> >>> My perl version:
> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >>> My computer:
> >>> Mac OS X Vesion 10.5.8
> >>>
> >>> I was following this preliminary steps:
> >>>
> >>> --------------
> >>>
> >>> PRELIMINARY PREPARATION
> >>>
> >>>    This is optional, but regardless of your subsequent choice of
> >>>    installation method, it will help to carry out the following steps.
> >>>    They will increase the likelyhood of installation success
> >>>    (especially of optional dependencies).
> >>>
> >>>      * Upgrade CPAN:
> >>>
> >>>  >perl -MCPAN -e shell
> >>>  cpan>install Bundle::CPAN
> >>>  cpan>q
> >>>
> >>>      * Install/upgrade Module::Build, and make it your preferred
> >>>        installer:
> >>>
> >>>  >cpan
> >>>  cpan>install Module::Build
> >>>  cpan>o conf prefer_installer MB
> >>>  cpan>o conf commit
> >>>  cpan>q
> >>>
> >>>      * Install the expat library by whatever method is
> >>>        appropriate for your system.
> >>>
> >>>      * If your expat library is installed in a non-standard location,
> >>>        tell CPAN about it:
> >>>
> >>>  >cpan
> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>>  cpan>o conf commit
> >>>
> >>> --------------
> >>>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> "some
> >>> problems". In text file you can see the whole process.
> >>> What did I do wrong?
> >>>
> >>>
> >>> After solving these preliminary steps, what should I do? What exactly
> >>> .tar
> >>> or .whatever should I download to install?
> >>>
> >>> I don't see the difference between installing it through "built.PL" or
> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
> >>> MAC.
> >>>
> >>> * I went to Fink webpage and what I expected to see was "hello!
> download
> >>> Bioperl simply clicking here!" but far from this, what it seems is that
> >>> first I have to download some kinf of Fink-program before starting with
> >>> Bioperl... is it something close to this?
> >>>
> >>> I'm sorry, too many questions... But I really want to learn to use
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>>
> >>> Thank you so much,
> >>>
> >>> Casandra
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> [hidden email]
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > [hidden email]
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

casandra-13
Ok, this is what happened. I guess this mean it worked, didn't it?

Last login: Tue Feb  7 22:47:16 on ttys000
maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
Can't locate Bio/SeqIO.pm in @INC (@INC contains:
/Users/mcasaandrariera/src/bioperl-live
/Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
/Network/Library/Perl/5.12/darwin-thread-multi-2level
/Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
/System/Library/Perl/5.12/darwin-thread-multi-2level
/System/Library/Perl/5.12
/System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.12 .) at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I took your src name (I hadn't any better suggestion, although I don't know
what src means... :P)

Thank you so much to all of you! I have to say that it was a big relief
reading Dave telling so simple things :D thanks!

Maybe it will be useless to explain it to me, but, why this method isn't
"installing" Bioperl? Why I didn't need to do all those preliminary steps,
use Fink, and so on? I mean, if I can finally do the same (using Bioperl).

And related to the previous method I tried, I read that you were discussing
"that she wants to use local::lib, but there need to be some prereqs
installed, but they can't be because she chose to use local::lib, and it's
not installed. " I really didn't "wanted" to use it, I chose it because it
was the default option, and, since I didn't know about the alternatives, I
thought that the default would be ok... But if what Dave said works, better
for me, I didn't really know what I was doing with thosesteps (but I want
to learn it soon! ;) )

Thank you all for your time ;)

Casandra

El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]>escribió:

> I will take the opportunity to shamelessly pimp my no-install install
> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
> Casandra is just looking to get started with BioPerl, messing with external
> libs and configs is probably overkill.
>
> Best,
> Dave
>
>
>
>  There’s a quickie, “zero-install” way to get BioPerl on your system.
>
>     1) Okay, click here to download bioperl as a zip file:
>
>     https://github.com/bioperl/bioperl-live/zipball/master
>
>
>     when it's done downloading, unzip it if your computer hasn’t done it
> automatically. On the
>     command line, you would do:
>
>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
>     or whatever the file is called. You should then have a folder with
> some ugly name like
>
>     bioperl-bioperl-live-558467a
>
>     3) rename that to
>
>     bioperl-live
>
>     4) move that folder to wherever you want to keep it. I keep mine in a
> directory called src in my
>         home directory.
>
>     So on my computer if I go to the command line and cd to that folder
> and type pwd I get:
>
>     /Users/dave/src/bioperl-live
>
>     5) in the terminal, cd to your home directory.
>
>     6) see if you have a file named .bash_profile by typing
>
>     ls -l ~/.bash_profile
>
>     7) if so, open that file in your favorite editor. if the file doesn't
> exist, just create the file.
>
>     8) put this line in your .bash_profile
>
>              export PERL5LIB=/Users/dave/src/bioperl-live
>
>     (obviously replacing my path info with wherever you chose to put
> bioperl)
>
>     9) save and close your .bash_profile
>
>   10) open a new terminal window so that the change will take effect.
>
>   11) on the command line of the new terminal, type
>
>                perl -e "use Bio::SeqIO;"
>
>     If that works, then you have "installed" bioperl. Yay!
>
>
>
>
>
>
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]> wrote:
>
>> Yes, but those doc don't address exactly the problem Cassandra is
>> having, that she wants to use local::lib, but there need to be some
>> prereqs installed, but they can't be because she chose to use
>> local::lib, and it's not installed.  That's all fine if you're not a
>> newbie and know how to properly install the prereqs before using the
>> cpan shell, but when following instructions that say "use local::lib",
>> I find that the instructions are completely insufficient in actually
>> getting the desired software installed.  Thus the need for a good
>> tutorial.
>>
>> Scott
>>
>>
>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]>
>> wrote:
>> > I guess one key question is where these CPAN installation instructions
>> come
>> > from.  They're a bit odd, and if this is from the wiki we need to do
>> some
>> > updating.
>> >
>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>> > single perl version.
>> >
>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>> >
>> > In my case I use perlbrew (which is all local by default, and allows
>> > switching between perl versions).  Highly recommend using either simple
>> > local::lib or perlbrew in combination with cpanm.
>> >
>> > https://metacpan.org/module/perlbrew
>> > https://metacpan.org/module/cpanm
>> >
>> > chris
>>
>> >
>> >
>> >
>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>> >>
>> >> hi Cassandra,
>> >>
>> >> I don't have an answer for you at the moment.  It seems to me that
>> >> using local::lib is a good idea, but I've never found a good tutorial
>> >> for using it, so I haven't.  Perhaps someone else on the list can
>> >> suggest one.
>> >>
>> >> The other thing I just wanted to mention as the admin that approved
>> >> your message--I came very close to deleting it from the queue without
>> >> looking at it because it is not unusual for spam messages to have
>> >> generic subjects like "help!"  (just for future reference :-)
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>  wrote:
>> >>>
>> >>> Hi,
>> >>>
>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>> >>> installed becaused I have already write some scripts but I'm biologist
>> >>> so...
>> >>> not pretty sure about what messages say.
>> >>>
>> >>> My perl version:
>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>> >>> My computer:
>> >>> Mac OS X Vesion 10.5.8
>> >>>
>> >>> I was following this preliminary steps:
>> >>>
>> >>> --------------
>> >>>
>> >>> PRELIMINARY PREPARATION
>> >>>
>> >>>    This is optional, but regardless of your subsequent choice of
>> >>>    installation method, it will help to carry out the following steps.
>> >>>    They will increase the likelyhood of installation success
>> >>>    (especially of optional dependencies).
>> >>>
>> >>>      * Upgrade CPAN:
>> >>>
>> >>>  >perl -MCPAN -e shell
>> >>>  cpan>install Bundle::CPAN
>> >>>  cpan>q
>> >>>
>> >>>      * Install/upgrade Module::Build, and make it your preferred
>> >>>        installer:
>> >>>
>> >>>  >cpan
>> >>>  cpan>install Module::Build
>> >>>  cpan>o conf prefer_installer MB
>> >>>  cpan>o conf commit
>> >>>  cpan>q
>> >>>
>> >>>      * Install the expat library by whatever method is
>> >>>        appropriate for your system.
>> >>>
>> >>>      * If your expat library is installed in a non-standard location,
>> >>>        tell CPAN about it:
>> >>>
>> >>>  >cpan
>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>> >>> EXPATINCPATH=/non-standard/include"
>> >>>  cpan>o conf commit
>> >>>
>> >>> --------------
>> >>>
>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>> one
>> >>> it
>> >>> started asking too many things to me, and finally it stopped due to
>> "some
>> >>> problems". In text file you can see the whole process.
>> >>> What did I do wrong?
>> >>>
>> >>>
>> >>> After solving these preliminary steps, what should I do? What exactly
>> >>> .tar
>> >>> or .whatever should I download to install?
>> >>>
>> >>> I don't see the difference between installing it through "built.PL" or
>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
>> >>> MAC.
>> >>>
>> >>> * I went to Fink webpage and what I expected to see was "hello!
>> download
>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>> that
>> >>> first I have to download some kinf of Fink-program before starting
>> with
>> >>> Bioperl... is it something close to this?
>> >>>
>> >>> I'm sorry, too many questions... But I really want to learn to use
>> >>> Bioperl
>> >>> but I have no people to ask it face to face.
>> >>>
>> >>> Thank you so much,
>> >>>
>> >>> Casandra
>> >>>
>> >>> _______________________________________________
>> >>> Bioperl-l mailing list
>> >>> [hidden email]
>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >>
>> >>
>> >>
>> >>
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > [hidden email]
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> [hidden email]
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>


--
Casandra Riera
+34 629774181
Barcelona, Spain.

[hidden email]
http://terrainsalo.blogspot.com/

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Warren W. Kretzschmar
Hi Cassandra,
Do make sure you follow steps 6-10 (below) because bioperl is not in your
include path yet.  Without adding bioperl to your include path, bioperl
will only work when you are running programs while in the bioperl-live
dir.  This is because the current dir is usually added to the perl include
list.

   6) see if you have a file named .bash_profile by typing

   ls -l ~/.bash_profile

   7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

   8) put this line in your .bash_profile

            export PERL5LIB=/Users/dave/src/
bioperl-live

   (obviously replacing my path info with wherever you chose to put
bioperl)

   9) save and close your .bash_profile

 10) open a new terminal window so that the change will take effect.

Warren
--
In God we trust, all others bring data. - William Edwards Deming


On Tue, Feb 7, 2012 at 10:05 PM, casandra <[hidden email]> wrote:

> Ok, this is what happened. I guess this mean it worked, didn't it?
>
> Last login: Tue Feb  7 22:47:16 on ttys000
> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
> /Users/mcasaandrariera/src/bioperl-live
> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
> /Network/Library/Perl/5.12/darwin-thread-multi-2level
> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
> /System/Library/Perl/5.12/darwin-thread-multi-2level
> /System/Library/Perl/5.12
> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.12 .) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
> maccasandra:bioperl-live mcasandrariera$
>
> I took your src name (I hadn't any better suggestion, although I don't know
> what src means... :P)
>
> Thank you so much to all of you! I have to say that it was a big relief
> reading Dave telling so simple things :D thanks!
>
> Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>
> And related to the previous method I tried, I read that you were discussing
> "that she wants to use local::lib, but there need to be some prereqs
> installed, but they can't be because she chose to use local::lib, and it's
> not installed. " I really didn't "wanted" to use it, I chose it because it
> was the default option, and, since I didn't know about the alternatives, I
> thought that the default would be ok... But if what Dave said works, better
> for me, I didn't really know what I was doing with thosesteps (but I want
> to learn it soon! ;) )
>
> Thank you all for your time ;)
>
> Casandra
>
> El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]
> >escribió:
>
> > I will take the opportunity to shamelessly pimp my no-install install
> > instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
> > Casandra is just looking to get started with BioPerl, messing with
> external
> > libs and configs is probably overkill.
> >
> > Best,
> > Dave
> >
> >
> >
> >  There’s a quickie, “zero-install” way to get BioPerl on your system.
> >
> >     1) Okay, click here to download bioperl as a zip file:
> >
> >     https://github.com/bioperl/bioperl-live/zipball/master
> >
> >
> >     when it's done downloading, unzip it if your computer hasn’t done it
> > automatically. On the
> >     command line, you would do:
> >
> >          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
> >
> >     or whatever the file is called. You should then have a folder with
> > some ugly name like
> >
> >     bioperl-bioperl-live-558467a
> >
> >     3) rename that to
> >
> >     bioperl-live
> >
> >     4) move that folder to wherever you want to keep it. I keep mine in a
> > directory called src in my
> >         home directory.
> >
> >     So on my computer if I go to the command line and cd to that folder
> > and type pwd I get:
> >
> >     /Users/dave/src/bioperl-live
> >
> >     5) in the terminal, cd to your home directory.
> >
> >     6) see if you have a file named .bash_profile by typing
> >
> >     ls -l ~/.bash_profile
> >
> >     7) if so, open that file in your favorite editor. if the file doesn't
> > exist, just create the file.
> >
> >     8) put this line in your .bash_profile
> >
> >              export PERL5LIB=/Users/dave/src/bioperl-live
> >
> >     (obviously replacing my path info with wherever you chose to put
> > bioperl)
> >
> >     9) save and close your .bash_profile
> >
> >   10) open a new terminal window so that the change will take effect.
> >
> >   11) on the command line of the new terminal, type
> >
> >                perl -e "use Bio::SeqIO;"
> >
> >     If that works, then you have "installed" bioperl. Yay!
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]> wrote:
> >
> >> Yes, but those doc don't address exactly the problem Cassandra is
> >> having, that she wants to use local::lib, but there need to be some
> >> prereqs installed, but they can't be because she chose to use
> >> local::lib, and it's not installed.  That's all fine if you're not a
> >> newbie and know how to properly install the prereqs before using the
> >> cpan shell, but when following instructions that say "use local::lib",
> >> I find that the instructions are completely insufficient in actually
> >> getting the desired software installed.  Thus the need for a good
> >> tutorial.
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]>
> >> wrote:
> >> > I guess one key question is where these CPAN installation instructions
> >> come
> >> > from.  They're a bit odd, and if this is from the wiki we need to do
> >> some
> >> > updating.
> >> >
> >> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> >> > single perl version.
> >> >
> >> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >> >
> >> > In my case I use perlbrew (which is all local by default, and allows
> >> > switching between perl versions).  Highly recommend using either
> simple
> >> > local::lib or perlbrew in combination with cpanm.
> >> >
> >> > https://metacpan.org/module/perlbrew
> >> > https://metacpan.org/module/cpanm
> >> >
> >> > chris
> >>
> >> >
> >> >
> >> >
> >> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >> >>
> >> >> hi Cassandra,
> >> >>
> >> >> I don't have an answer for you at the moment.  It seems to me that
> >> >> using local::lib is a good idea, but I've never found a good tutorial
> >> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> >> suggest one.
> >> >>
> >> >> The other thing I just wanted to mention as the admin that approved
> >> >> your message--I came very close to deleting it from the queue without
> >> >> looking at it because it is not unusual for spam messages to have
> >> >> generic subjects like "help!"  (just for future reference :-)
> >> >>
> >> >> Scott
> >> >>
> >> >>
> >> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>
>  wrote:
> >> >>>
> >> >>> Hi,
> >> >>>
> >> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >> >>> installed becaused I have already write some scripts but I'm
> biologist
> >> >>> so...
> >> >>> not pretty sure about what messages say.
> >> >>>
> >> >>> My perl version:
> >> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >> >>> My computer:
> >> >>> Mac OS X Vesion 10.5.8
> >> >>>
> >> >>> I was following this preliminary steps:
> >> >>>
> >> >>> --------------
> >> >>>
> >> >>> PRELIMINARY PREPARATION
> >> >>>
> >> >>>    This is optional, but regardless of your subsequent choice of
> >> >>>    installation method, it will help to carry out the following
> steps.
> >> >>>    They will increase the likelyhood of installation success
> >> >>>    (especially of optional dependencies).
> >> >>>
> >> >>>      * Upgrade CPAN:
> >> >>>
> >> >>>  >perl -MCPAN -e shell
> >> >>>  cpan>install Bundle::CPAN
> >> >>>  cpan>q
> >> >>>
> >> >>>      * Install/upgrade Module::Build, and make it your preferred
> >> >>>        installer:
> >> >>>
> >> >>>  >cpan
> >> >>>  cpan>install Module::Build
> >> >>>  cpan>o conf prefer_installer MB
> >> >>>  cpan>o conf commit
> >> >>>  cpan>q
> >> >>>
> >> >>>      * Install the expat library by whatever method is
> >> >>>        appropriate for your system.
> >> >>>
> >> >>>      * If your expat library is installed in a non-standard
> location,
> >> >>>        tell CPAN about it:
> >> >>>
> >> >>>  >cpan
> >> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >> >>> EXPATINCPATH=/non-standard/include"
> >> >>>  cpan>o conf commit
> >> >>>
> >> >>> --------------
> >> >>>
> >> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
> >> one
> >> >>> it
> >> >>> started asking too many things to me, and finally it stopped due to
> >> "some
> >> >>> problems". In text file you can see the whole process.
> >> >>> What did I do wrong?
> >> >>>
> >> >>>
> >> >>> After solving these preliminary steps, what should I do? What
> exactly
> >> >>> .tar
> >> >>> or .whatever should I download to install?
> >> >>>
> >> >>> I don't see the difference between installing it through "built.PL"
> or
> >> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff
> for
> >> >>> MAC.
> >> >>>
> >> >>> * I went to Fink webpage and what I expected to see was "hello!
> >> download
> >> >>> Bioperl simply clicking here!" but far from this, what it seems is
> >> that
> >> >>> first I have to download some kinf of Fink-program before starting
> >> with
> >> >>> Bioperl... is it something close to this?
> >> >>>
> >> >>> I'm sorry, too many questions... But I really want to learn to use
> >> >>> Bioperl
> >> >>> but I have no people to ask it face to face.
> >> >>>
> >> >>> Thank you so much,
> >> >>>
> >> >>> Casandra
> >> >>>
> >> >>> _______________________________________________
> >> >>> Bioperl-l mailing list
> >> >>> [hidden email]
> >> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >> >>
> >> >>
> >> >>
> >> >>
> >> >
> >> > _______________________________________________
> >> > Bioperl-l mailing list
> >> > [hidden email]
> >> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >> --
> >> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.                                   scott at scottcain
> >> dot net
> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >> Ontario Institute for Cancer Research
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> [hidden email]
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
>
>
> --
> Casandra Riera
> +34 629774181
> Barcelona, Spain.
>
> [hidden email]
> http://terrainsalo.blogspot.com/
>
> _______________________________________________
> Bioperl-l mailing list
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Dave Messina-3
In reply to this post by casandra-13
Hi Casandra,

(Wayne already answered this much more succinctly than me, but here is my
answer anyway.)


I think you're almost there.

The fact that you get no error message when you type
perl -e "use Bio::SeqIO;"

in the directory src/bioperl-live/ tells me that probably Perl doesn't
"see" where you put BioPerl. That's what the PERL5LIB variable does; it
tells Perl that it should look for Perl modules in the directories named in
the environmental variable PERL5LIB.

If you type

printenv PERL5LIB

do you see

/Users/mcasandrariera/src/bioperl-live

?

If not, then redo steps 5-10 and then try typing
printenv PERL5LIB

again. Make sure that in step 8, instead of

export PERL5LIB=/Users/dave/src/bioperl-live

you type

export PERL5LIB=/Users/mcasandrariera/src/bioperl-live


To answer your other questions:

although I don't know what src means...


src is just a directory name. It's short for "source", which itself is
really short for "source code". src the name of the directory where I keep
all of my source code libraries like BioPerl.


Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>

The short answer is that by following the zero-install instructions, you
won't be able use some parts of BioPerl (which I'm betting you won't need
right away).

Chris and Scott's advice is correct and the right way to go in the long
run. Once you've gotten your feet wet a bit and become more familiar with
Perl and BioPerl, you may want to come back to their approach and try it
again.


Best,
Dave






On Tue, Feb 7, 2012 at 23:05, casandra <[hidden email]> wrote:

> Ok, this is what happened. I guess this mean it worked, didn't it?
>
> Last login: Tue Feb  7 22:47:16 on ttys000
> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
> /Users/mcasaandrariera/src/bioperl-live
> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
> /Network/Library/Perl/5.12/darwin-thread-multi-2level
> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
> /System/Library/Perl/5.12/darwin-thread-multi-2level
> /System/Library/Perl/5.12
> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.12 .) at -e line 1.
> BEGIN failed--compilation aborted at -e line 1.
> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
> maccasandra:bioperl-live mcasandrariera$
>
> I took your src name (I hadn't any better suggestion, although I don't
> know what src means... :P)
>
> Thank you so much to all of you! I have to say that it was a big relief
> reading Dave telling so simple things :D thanks!
>
> Maybe it will be useless to explain it to me, but, why this method isn't
> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>
> And related to the previous method I tried, I read that you were
> discussing "that she wants to use local::lib, but there need to be
> some prereqs installed, but they can't be because she chose to
> use local::lib, and it's not installed. " I really didn't "wanted" to use
> it, I chose it because it was the default option, and, since I didn't know
> about the alternatives, I thought that the default would be ok... But if
> what Dave said works, better for me, I didn't really know what I was doing
> with thosesteps (but I want to learn it soon! ;) )
>
> Thank you all for your time ;)
>
> Casandra
>
> El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]>escribió:
>
> I will take the opportunity to shamelessly pimp my no-install install
>> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
>> Casandra is just looking to get started with BioPerl, messing with external
>> libs and configs is probably overkill.
>>
>> Best,
>> Dave
>>
>>
>>
>>  There’s a quickie, “zero-install” way to get BioPerl on your system.
>>
>>     1) Okay, click here to download bioperl as a zip file:
>>
>>     https://github.com/bioperl/bioperl-live/zipball/master
>>
>>
>>     when it's done downloading, unzip it if your computer hasn’t done it
>> automatically. On the
>>     command line, you would do:
>>
>>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>>
>>     or whatever the file is called. You should then have a folder with
>> some ugly name like
>>
>>     bioperl-bioperl-live-558467a
>>
>>     3) rename that to
>>
>>     bioperl-live
>>
>>     4) move that folder to wherever you want to keep it. I keep mine in a
>> directory called src in my
>>         home directory.
>>
>>     So on my computer if I go to the command line and cd to that folder
>> and type pwd I get:
>>
>>     /Users/dave/src/bioperl-live
>>
>>     5) in the terminal, cd to your home directory.
>>
>>     6) see if you have a file named .bash_profile by typing
>>
>>     ls -l ~/.bash_profile
>>
>>     7) if so, open that file in your favorite editor. if the file doesn't
>> exist, just create the file.
>>
>>     8) put this line in your .bash_profile
>>
>>              export PERL5LIB=/Users/dave/src/bioperl-live
>>
>>     (obviously replacing my path info with wherever you chose to put
>> bioperl)
>>
>>     9) save and close your .bash_profile
>>
>>   10) open a new terminal window so that the change will take effect.
>>
>>   11) on the command line of the new terminal, type
>>
>>                perl -e "use Bio::SeqIO;"
>>
>>     If that works, then you have "installed" bioperl. Yay!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]> wrote:
>>
>>> Yes, but those doc don't address exactly the problem Cassandra is
>>> having, that she wants to use local::lib, but there need to be some
>>> prereqs installed, but they can't be because she chose to use
>>> local::lib, and it's not installed.  That's all fine if you're not a
>>> newbie and know how to properly install the prereqs before using the
>>> cpan shell, but when following instructions that say "use local::lib",
>>> I find that the instructions are completely insufficient in actually
>>> getting the desired software installed.  Thus the need for a good
>>> tutorial.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]>
>>> wrote:
>>> > I guess one key question is where these CPAN installation instructions
>>> come
>>> > from.  They're a bit odd, and if this is from the wiki we need to do
>>> some
>>> > updating.
>>> >
>>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>>> > single perl version.
>>> >
>>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>> >
>>> > In my case I use perlbrew (which is all local by default, and allows
>>> > switching between perl versions).  Highly recommend using either simple
>>> > local::lib or perlbrew in combination with cpanm.
>>> >
>>> > https://metacpan.org/module/perlbrew
>>> > https://metacpan.org/module/cpanm
>>> >
>>> > chris
>>>
>>> >
>>> >
>>> >
>>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>> >>
>>> >> hi Cassandra,
>>> >>
>>> >> I don't have an answer for you at the moment.  It seems to me that
>>> >> using local::lib is a good idea, but I've never found a good tutorial
>>> >> for using it, so I haven't.  Perhaps someone else on the list can
>>> >> suggest one.
>>> >>
>>> >> The other thing I just wanted to mention as the admin that approved
>>> >> your message--I came very close to deleting it from the queue without
>>> >> looking at it because it is not unusual for spam messages to have
>>> >> generic subjects like "help!"  (just for future reference :-)
>>> >>
>>> >> Scott
>>> >>
>>> >>
>>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>
>>>  wrote:
>>> >>>
>>> >>> Hi,
>>> >>>
>>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>> >>> installed becaused I have already write some scripts but I'm
>>> biologist
>>> >>> so...
>>> >>> not pretty sure about what messages say.
>>> >>>
>>> >>> My perl version:
>>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>> >>> My computer:
>>> >>> Mac OS X Vesion 10.5.8
>>> >>>
>>> >>> I was following this preliminary steps:
>>> >>>
>>> >>> --------------
>>> >>>
>>> >>> PRELIMINARY PREPARATION
>>> >>>
>>> >>>    This is optional, but regardless of your subsequent choice of
>>> >>>    installation method, it will help to carry out the following
>>> steps.
>>> >>>    They will increase the likelyhood of installation success
>>> >>>    (especially of optional dependencies).
>>> >>>
>>> >>>      * Upgrade CPAN:
>>> >>>
>>> >>>  >perl -MCPAN -e shell
>>> >>>  cpan>install Bundle::CPAN
>>> >>>  cpan>q
>>> >>>
>>> >>>      * Install/upgrade Module::Build, and make it your preferred
>>> >>>        installer:
>>> >>>
>>> >>>  >cpan
>>> >>>  cpan>install Module::Build
>>> >>>  cpan>o conf prefer_installer MB
>>> >>>  cpan>o conf commit
>>> >>>  cpan>q
>>> >>>
>>> >>>      * Install the expat library by whatever method is
>>> >>>        appropriate for your system.
>>> >>>
>>> >>>      * If your expat library is installed in a non-standard location,
>>> >>>        tell CPAN about it:
>>> >>>
>>> >>>  >cpan
>>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>> >>> EXPATINCPATH=/non-standard/include"
>>> >>>  cpan>o conf commit
>>> >>>
>>> >>> --------------
>>> >>>
>>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>>> one
>>> >>> it
>>> >>> started asking too many things to me, and finally it stopped due to
>>> "some
>>> >>> problems". In text file you can see the whole process.
>>> >>> What did I do wrong?
>>> >>>
>>> >>>
>>> >>> After solving these preliminary steps, what should I do? What exactly
>>> >>> .tar
>>> >>> or .whatever should I download to install?
>>> >>>
>>> >>> I don't see the difference between installing it through "built.PL"
>>> or
>>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
>>> >>> MAC.
>>> >>>
>>> >>> * I went to Fink webpage and what I expected to see was "hello!
>>> download
>>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>>> that
>>> >>> first I have to download some kinf of Fink-program before starting
>>> with
>>> >>> Bioperl... is it something close to this?
>>> >>>
>>> >>> I'm sorry, too many questions... But I really want to learn to use
>>> >>> Bioperl
>>> >>> but I have no people to ask it face to face.
>>> >>>
>>> >>> Thank you so much,
>>> >>>
>>> >>> Casandra
>>> >>>
>>> >>> _______________________________________________
>>> >>> Bioperl-l mailing list
>>> >>> [hidden email]
>>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> >>
>>> >>
>>> >>
>>> >>
>>> >
>>> > _______________________________________________
>>> > Bioperl-l mailing list
>>> > [hidden email]
>>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>
>
> --
> Casandra Riera
> +34 629774181
> Barcelona, Spain.
>
> [hidden email]
> http://terrainsalo.blogspot.com/
>
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

casandra-13
Thank you both,
before I received Dave's email I was answering the following:

Hello Warren,

I've repeated those steps just in case, here I show you:

maccasandra:~ mcasandrariera$ vi .bash_profile
maccasandra:~ mcasandrariera$ more .bash_profile
export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
maccasandra:bioperl-live mcasandrariera$

I get the same "result". Am I supposed to get something different?"

And now I tried what Dave ask me:

maccasandra:bioperl-live mcasandrariera$ printenv PERL5LIB
/Users/mcasandrariera/src/bioperl-live
maccasandra:bioperl-live mcasandrariera$

I have to say it's very nice from you to help me, specially you, Dave, who
translates all this into casandra's-super-dummie language..

Cas.

El 7 de febrero de 2012 23:39, Dave Messina <[hidden email]>escribió:

> Hi Casandra,
>
> (Wayne already answered this much more succinctly than me, but here is my
> answer anyway.)
>
>
> I think you're almost there.
>
> The fact that you get no error message when you type
>  perl -e "use Bio::SeqIO;"
>
> in the directory src/bioperl-live/ tells me that probably Perl doesn't
> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
> tells Perl that it should look for Perl modules in the directories named in
> the environmental variable PERL5LIB.
>
> If you type
>
> printenv PERL5LIB
>
> do you see
>
> /Users/mcasandrariera/src/bioperl-live
>
> ?
>
> If not, then redo steps 5-10 and then try typing
> printenv PERL5LIB
>
> again. Make sure that in step 8, instead of
>
> export PERL5LIB=/Users/dave/src/bioperl-live
>
> you type
>
> export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
>
>
> To answer your other questions:
>
> although I don't know what src means...
>
>
> src is just a directory name. It's short for "source", which itself is
> really short for "source code". src the name of the directory where I keep
> all of my source code libraries like BioPerl.
>
>
> Maybe it will be useless to explain it to me, but, why this method isn't
>> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
>> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>>
>
> The short answer is that by following the zero-install instructions, you
> won't be able use some parts of BioPerl (which I'm betting you won't need
> right away).
>
> Chris and Scott's advice is correct and the right way to go in the long
> run. Once you've gotten your feet wet a bit and become more familiar with
> Perl and BioPerl, you may want to come back to their approach and try it
> again.
>
>
> Best,
> Dave
>
>
>
>
>
>
> On Tue, Feb 7, 2012 at 23:05, casandra <[hidden email]> wrote:
>
>> Ok, this is what happened. I guess this mean it worked, didn't it?
>>
>> Last login: Tue Feb  7 22:47:16 on ttys000
>> maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>> Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>> /Users/mcasaandrariera/src/bioperl-live
>> /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
>> /Network/Library/Perl/5.12/darwin-thread-multi-2level
>> /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>> /System/Library/Perl/5.12/darwin-thread-multi-2level
>> /System/Library/Perl/5.12
>> /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
>> /System/Library/Perl/Extras/5.12 .) at -e line 1.
>> BEGIN failed--compilation aborted at -e line 1.
>> maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>> maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>> maccasandra:bioperl-live mcasandrariera$
>>
>> I took your src name (I hadn't any better suggestion, although I don't
>> know what src means... :P)
>>
>> Thank you so much to all of you! I have to say that it was a big relief
>> reading Dave telling so simple things :D thanks!
>>
>> Maybe it will be useless to explain it to me, but, why this method isn't
>> "installing" Bioperl? Why I didn't need to do all those preliminary steps,
>> use Fink, and so on? I mean, if I can finally do the same (using Bioperl).
>>
>> And related to the previous method I tried, I read that you were
>> discussing "that she wants to use local::lib, but there need to be
>> some prereqs installed, but they can't be because she chose to
>> use local::lib, and it's not installed. " I really didn't "wanted" to use
>> it, I chose it because it was the default option, and, since I didn't know
>> about the alternatives, I thought that the default would be ok... But if
>> what Dave said works, better for me, I didn't really know what I was doing
>> with thosesteps (but I want to learn it soon! ;) )
>>
>> Thank you all for your time ;)
>>
>> Casandra
>>
>> El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]>escribió:
>>
>> I will take the opportunity to shamelessly pimp my no-install install
>>> instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
>>> Casandra is just looking to get started with BioPerl, messing with external
>>> libs and configs is probably overkill.
>>>
>>> Best,
>>> Dave
>>>
>>>
>>>
>>>  There’s a quickie, “zero-install” way to get BioPerl on your system.
>>>
>>>     1) Okay, click here to download bioperl as a zip file:
>>>
>>>     https://github.com/bioperl/bioperl-live/zipball/master
>>>
>>>
>>>     when it's done downloading, unzip it if your computer hasn’t done it
>>> automatically. On the
>>>     command line, you would do:
>>>
>>>          unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>>>
>>>     or whatever the file is called. You should then have a folder with
>>> some ugly name like
>>>
>>>     bioperl-bioperl-live-558467a
>>>
>>>     3) rename that to
>>>
>>>     bioperl-live
>>>
>>>     4) move that folder to wherever you want to keep it. I keep mine in
>>> a directory called src in my
>>>         home directory.
>>>
>>>     So on my computer if I go to the command line and cd to that folder
>>> and type pwd I get:
>>>
>>>     /Users/dave/src/bioperl-live
>>>
>>>     5) in the terminal, cd to your home directory.
>>>
>>>     6) see if you have a file named .bash_profile by typing
>>>
>>>     ls -l ~/.bash_profile
>>>
>>>     7) if so, open that file in your favorite editor. if the file
>>> doesn't exist, just create the file.
>>>
>>>     8) put this line in your .bash_profile
>>>
>>>              export PERL5LIB=/Users/dave/src/bioperl-live
>>>
>>>     (obviously replacing my path info with wherever you chose to put
>>> bioperl)
>>>
>>>     9) save and close your .bash_profile
>>>
>>>   10) open a new terminal window so that the change will take effect.
>>>
>>>   11) on the command line of the new terminal, type
>>>
>>>                perl -e "use Bio::SeqIO;"
>>>
>>>     If that works, then you have "installed" bioperl. Yay!
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]> wrote:
>>>
>>>> Yes, but those doc don't address exactly the problem Cassandra is
>>>> having, that she wants to use local::lib, but there need to be some
>>>> prereqs installed, but they can't be because she chose to use
>>>> local::lib, and it's not installed.  That's all fine if you're not a
>>>> newbie and know how to properly install the prereqs before using the
>>>> cpan shell, but when following instructions that say "use local::lib",
>>>> I find that the instructions are completely insufficient in actually
>>>> getting the desired software installed.  Thus the need for a good
>>>> tutorial.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <[hidden email]>
>>>> wrote:
>>>> > I guess one key question is where these CPAN installation
>>>> instructions come
>>>> > from.  They're a bit odd, and if this is from the wiki we need to do
>>>> some
>>>> > updating.
>>>> >
>>>> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
>>>> > single perl version.
>>>> >
>>>> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
>>>> >
>>>> > In my case I use perlbrew (which is all local by default, and allows
>>>> > switching between perl versions).  Highly recommend using either
>>>> simple
>>>> > local::lib or perlbrew in combination with cpanm.
>>>> >
>>>> > https://metacpan.org/module/perlbrew
>>>> > https://metacpan.org/module/cpanm
>>>> >
>>>> > chris
>>>>
>>>> >
>>>> >
>>>> >
>>>> > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>>> >>
>>>> >> hi Cassandra,
>>>> >>
>>>> >> I don't have an answer for you at the moment.  It seems to me that
>>>> >> using local::lib is a good idea, but I've never found a good tutorial
>>>> >> for using it, so I haven't.  Perhaps someone else on the list can
>>>> >> suggest one.
>>>> >>
>>>> >> The other thing I just wanted to mention as the admin that approved
>>>> >> your message--I came very close to deleting it from the queue without
>>>> >> looking at it because it is not unusual for spam messages to have
>>>> >> generic subjects like "help!"  (just for future reference :-)
>>>> >>
>>>> >> Scott
>>>> >>
>>>> >>
>>>> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<[hidden email]>
>>>>  wrote:
>>>> >>>
>>>> >>> Hi,
>>>> >>>
>>>> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
>>>> >>> installed becaused I have already write some scripts but I'm
>>>> biologist
>>>> >>> so...
>>>> >>> not pretty sure about what messages say.
>>>> >>>
>>>> >>> My perl version:
>>>> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>>> >>> My computer:
>>>> >>> Mac OS X Vesion 10.5.8
>>>> >>>
>>>> >>> I was following this preliminary steps:
>>>> >>>
>>>> >>> --------------
>>>> >>>
>>>> >>> PRELIMINARY PREPARATION
>>>> >>>
>>>> >>>    This is optional, but regardless of your subsequent choice of
>>>> >>>    installation method, it will help to carry out the following
>>>> steps.
>>>> >>>    They will increase the likelyhood of installation success
>>>> >>>    (especially of optional dependencies).
>>>> >>>
>>>> >>>      * Upgrade CPAN:
>>>> >>>
>>>> >>>  >perl -MCPAN -e shell
>>>> >>>  cpan>install Bundle::CPAN
>>>> >>>  cpan>q
>>>> >>>
>>>> >>>      * Install/upgrade Module::Build, and make it your preferred
>>>> >>>        installer:
>>>> >>>
>>>> >>>  >cpan
>>>> >>>  cpan>install Module::Build
>>>> >>>  cpan>o conf prefer_installer MB
>>>> >>>  cpan>o conf commit
>>>> >>>  cpan>q
>>>> >>>
>>>> >>>      * Install the expat library by whatever method is
>>>> >>>        appropriate for your system.
>>>> >>>
>>>> >>>      * If your expat library is installed in a non-standard
>>>> location,
>>>> >>>        tell CPAN about it:
>>>> >>>
>>>> >>>  >cpan
>>>> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>>>> >>> EXPATINCPATH=/non-standard/include"
>>>> >>>  cpan>o conf commit
>>>> >>>
>>>> >>> --------------
>>>> >>>
>>>> >>> And I think I did "Upgrade CPAN properly" but when I tried the next
>>>> one
>>>> >>> it
>>>> >>> started asking too many things to me, and finally it stopped due to
>>>> "some
>>>> >>> problems". In text file you can see the whole process.
>>>> >>> What did I do wrong?
>>>> >>>
>>>> >>>
>>>> >>> After solving these preliminary steps, what should I do? What
>>>> exactly
>>>> >>> .tar
>>>> >>> or .whatever should I download to install?
>>>> >>>
>>>> >>> I don't see the difference between installing it through "built.PL"
>>>> or
>>>> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff
>>>> for
>>>> >>> MAC.
>>>> >>>
>>>> >>> * I went to Fink webpage and what I expected to see was "hello!
>>>> download
>>>> >>> Bioperl simply clicking here!" but far from this, what it seems is
>>>> that
>>>> >>> first I have to download some kinf of Fink-program before starting
>>>> with
>>>> >>> Bioperl... is it something close to this?
>>>> >>>
>>>> >>> I'm sorry, too many questions... But I really want to learn to use
>>>> >>> Bioperl
>>>> >>> but I have no people to ask it face to face.
>>>> >>>
>>>> >>> Thank you so much,
>>>> >>>
>>>> >>> Casandra
>>>> >>>
>>>> >>> _______________________________________________
>>>> >>> Bioperl-l mailing list
>>>> >>> [hidden email]
>>>> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> >>
>>>> >>
>>>> >>
>>>> >>
>>>> >
>>>> > _______________________________________________
>>>> > Bioperl-l mailing list
>>>> > [hidden email]
>>>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain
>>>> dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> [hidden email]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>
>>>
>>
>>
>> --
>> Casandra Riera
>> +34 629774181
>> Barcelona, Spain.
>>
>> [hidden email]
>> http://terrainsalo.blogspot.com/
>>
>>
>


--
Casandra Riera
+34 629774181
Barcelona, Spain.

[hidden email]
http://terrainsalo.blogspot.com/

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Fields, Christopher J
In reply to this post by Dave Messina-3
The catch with a PERL5LIB approach for a new installation is the very
possibility that non-core dependencies will not be installed.  We'll
have a response down the road for 'why did Bio::Foo fail with the
following error', with an obvious missing dependency being the problem.

We've been discussing this on IRC (scott, leont and I). I tend to think
the best solution for new users is to set them up with both local::lib
and cpanm initially, either by simply documenting this or by getting a
script up and running for them.  This will resolve down-stream problems
(for instance, if the distribution is split up).

chris


On 02/07/2012 04:39 PM, Dave Messina wrote:

> Hi Casandra,
>
> (Wayne already answered this much more succinctly than me, but here is
> my answer anyway.)
>
>
> I think you're almost there.
>
> The fact that you get no error message when you type
> perl -e "use Bio::SeqIO;"
>
> in the directory src/bioperl-live/ tells me that probably Perl doesn't
> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
> tells Perl that it should look for Perl modules in the directories named
> in the environmental variable PERL5LIB.
>
> If you type
>
> printenv PERL5LIB
>
> do you see
>
> /Users/mcasandrariera/src/bioperl-live
>
> ?
>
> If not, then redo steps 5-10 and then try typing
> printenv PERL5LIB
>
> again. Make sure that in step 8, instead of
>
> export PERL5LIB=/Users/dave/src/bioperl-live
>
> you type
>
> export PERL5LIB=/Users/mcasandrariera/src/bioperl-live
>
>
> To answer your other questions:
>
>     although I don't know what src means...
>
>
> src is just a directory name. It's short for "source", which itself is
> really short for "source code". src the name of the directory where I
> keep all of my source code libraries like BioPerl.
>
>
>     Maybe it will be useless to explain it to me, but, why this method
>     isn't "installing" Bioperl? Why I didn't need to do all those
>     preliminary steps, use Fink, and so on? I mean, if I can finally do
>     the same (using Bioperl).
>
>
> The short answer is that by following the zero-install instructions, you
> won't be able use some parts of BioPerl (which I'm betting you won't
> need right away).
>
> Chris and Scott's advice is correct and the right way to go in the long
> run. Once you've gotten your feet wet a bit and become more familiar
> with Perl and BioPerl, you may want to come back to their approach and
> try it again.
>
>
> Best,
> Dave
>
>
>
>
>
> On Tue, Feb 7, 2012 at 23:05, casandra <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Ok, this is what happened. I guess this mean it worked, didn't it?
>
>     Last login: Tue Feb 7 22:47:16 on ttys000
>     maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>     Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>     /Users/mcasaandrariera/src/bioperl-live
>     /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12
>     /Network/Library/Perl/5.12/darwin-thread-multi-2level
>     /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>     /System/Library/Perl/5.12/darwin-thread-multi-2level
>     /System/Library/Perl/5.12
>     /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level
>     /System/Library/Perl/Extras/5.12 .) at -e line 1.
>     BEGIN failed--compilation aborted at -e line 1.
>     maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>     maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>     maccasandra:bioperl-live mcasandrariera$
>
>     I took your src name (I hadn't any better suggestion, although I
>     don't know what src means... :P)
>
>     Thank you so much to all of you! I have to say that it was a big
>     relief reading Dave telling so simple things :D thanks!
>
>     Maybe it will be useless to explain it to me, but, why this method
>     isn't "installing" Bioperl? Why I didn't need to do all those
>     preliminary steps, use Fink, and so on? I mean, if I can finally do
>     the same (using Bioperl).
>
>     And related to the previous method I tried, I read that you were
>     discussing "that she wants to use local::lib, but there need to be
>     some prereqs installed, but they can't be because she chose to use
>     local::lib, and it's not installed. " I really didn't "wanted" to
>     use it, I chose it because it was the default option, and, since I
>     didn't know about the alternatives, I thought that the default would
>     be ok... But if what Dave said works, better for me, I didn't really
>     know what I was doing with thosesteps (but I want to learn it soon! ;) )
>
>     Thank you all for your time ;)
>
>     Casandra
>
>     El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]
>     <mailto:[hidden email]>> escribió:
>
>         I will take the opportunity to shamelessly pimp my no-install
>         install instructions (below and
>         http://seqxml.org/xml/BioPerl.html). IMHO if Casandra is just
>         looking to get started with BioPerl, messing with external libs
>         and configs is probably overkill.
>
>         Best,
>         Dave
>
>
>
>         There’s a quickie, “zero-install” way to get BioPerl on your system.
>         1) Okay, click here to download bioperl as a zip file:
>
>         https://github.com/bioperl/bioperl-live/zipball/master
>
>
>         when it's done downloading, unzip it if your computer hasn’t
>         done it automatically. On the
>         command line, you would do:
>
>         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
>         or whatever the file is called. You should then have a folder
>         with some ugly name like
>
>         bioperl-bioperl-live-558467a
>
>         3) rename that to
>
>         bioperl-live
>
>         4) move that folder to wherever you want to keep it. I keep mine
>         in a directory called src in my
>         home directory.
>
>         So on my computer if I go to the command line and cd to that
>         folder and type pwd I get:
>
>         /Users/dave/src/bioperl-live
>
>         5) in the terminal, cd to your home directory.
>
>         6) see if you have a file named .bash_profile by typing
>
>         ls -l ~/.bash_profile
>
>         7) if so, open that file in your favorite editor. if the file
>         doesn't exist, just create the file.
>
>         8) put this line in your .bash_profile
>
>         export PERL5LIB=/Users/dave/src/bioperl-live
>
>         (obviously replacing my path info with wherever you chose to put
>         bioperl)
>
>         9) save and close your .bash_profile
>
>         10) open a new terminal window so that the change will take effect.
>
>         11) on the command line of the new terminal, type
>
>         perl -e "use Bio::SeqIO;"
>
>         If that works, then you have "installed" bioperl. Yay!
>
>
>
>
>
>
>
>
>
>
>
>
>         On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]
>         <mailto:[hidden email]>> wrote:
>
>             Yes, but those doc don't address exactly the problem
>             Cassandra is
>             having, that she wants to use local::lib, but there need to
>             be some
>             prereqs installed, but they can't be because she chose to use
>             local::lib, and it's not installed. That's all fine if
>             you're not a
>             newbie and know how to properly install the prereqs before
>             using the
>             cpan shell, but when following instructions that say "use
>             local::lib",
>             I find that the instructions are completely insufficient in
>             actually
>             getting the desired software installed. Thus the need for a good
>             tutorial.
>
>             Scott
>
>
>             On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields
>             <[hidden email] <mailto:[hidden email]>> wrote:
>              > I guess one key question is where these CPAN installation
>             instructions come
>              > from. They're a bit odd, and if this is from the wiki we
>             need to do some
>              > updating.
>              >
>              > Re: local::lib, the docs on CPAN are pretty nice if one
>             wants to use a
>              > single perl version.
>              >
>              >
>             https://metacpan.org/module/local::lib#The-bootstrapping-technique
>              >
>              > In my case I use perlbrew (which is all local by default,
>             and allows
>              > switching between perl versions). Highly recommend using
>             either simple
>              > local::lib or perlbrew in combination with cpanm.
>              >
>              > https://metacpan.org/module/perlbrew
>              > https://metacpan.org/module/cpanm
>              >
>              > chris
>
>              >
>              >
>              >
>              > On 02/07/2012 02:55 PM, Scott Cain wrote:
>              >>
>              >> hi Cassandra,
>              >>
>              >> I don't have an answer for you at the moment. It seems
>             to me that
>              >> using local::lib is a good idea, but I've never found a
>             good tutorial
>              >> for using it, so I haven't. Perhaps someone else on the
>             list can
>              >> suggest one.
>              >>
>              >> The other thing I just wanted to mention as the admin
>             that approved
>              >> your message--I came very close to deleting it from the
>             queue without
>              >> looking at it because it is not unusual for spam
>             messages to have
>              >> generic subjects like "help!" (just for future reference :-)
>              >>
>              >> Scott
>              >>
>              >>
>              >> On Tue, Feb 7, 2012 at 11:11 AM,
>             Casandra<[hidden email] <mailto:[hidden email]>>
>             wrote:
>              >>>
>              >>> Hi,
>              >>>
>              >>> I'm trying to install Bioperl but I'm a bit lost. I
>             know I have perl
>              >>> installed becaused I have already write some scripts
>             but I'm biologist
>              >>> so...
>              >>> not pretty sure about what messages say.
>              >>>
>              >>> My perl version:
>              >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>              >>> My computer:
>              >>> Mac OS X Vesion 10.5.8
>              >>>
>              >>> I was following this preliminary steps:
>              >>>
>              >>> --------------
>              >>>
>              >>> PRELIMINARY PREPARATION
>              >>>
>              >>> This is optional, but regardless of your subsequent
>             choice of
>              >>> installation method, it will help to carry out the
>             following steps.
>              >>> They will increase the likelyhood of installation success
>              >>> (especially of optional dependencies).
>              >>>
>              >>> * Upgrade CPAN:
>              >>>
>              >>> >perl -MCPAN -e shell
>              >>> cpan>install Bundle::CPAN
>              >>> cpan>q
>              >>>
>              >>> * Install/upgrade Module::Build, and make it your preferred
>              >>> installer:
>              >>>
>              >>> >cpan
>              >>> cpan>install Module::Build
>              >>> cpan>o conf prefer_installer MB
>              >>> cpan>o conf commit
>              >>> cpan>q
>              >>>
>              >>> * Install the expat library by whatever method is
>              >>> appropriate for your system.
>              >>>
>              >>> * If your expat library is installed in a non-standard
>             location,
>              >>> tell CPAN about it:
>              >>>
>              >>> >cpan
>              >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
>              >>> EXPATINCPATH=/non-standard/include"
>              >>> cpan>o conf commit
>              >>>
>              >>> --------------
>              >>>
>              >>> And I think I did "Upgrade CPAN properly" but when I
>             tried the next one
>              >>> it
>              >>> started asking too many things to me, and finally it
>             stopped due to "some
>              >>> problems". In text file you can see the whole process.
>              >>> What did I do wrong?
>              >>>
>              >>>
>              >>> After solving these preliminary steps, what should I
>             do? What exactly
>              >>> .tar
>              >>> or .whatever should I download to install?
>              >>>
>              >>> I don't see the difference between installing it
>             through "built.PL" or
>              >>> CPAN. And I don't know if I should do this or that
>             "Fink*" stuff for
>              >>> MAC.
>              >>>
>              >>> * I went to Fink webpage and what I expected to see was
>             "hello! download
>              >>> Bioperl simply clicking here!" but far from this, what
>             it seems is that
>              >>> first I have to download some kinf of Fink-program
>             before starting with
>              >>> Bioperl... is it something close to this?
>              >>>
>              >>> I'm sorry, too many questions... But I really want to
>             learn to use
>              >>> Bioperl
>              >>> but I have no people to ask it face to face.
>              >>>
>              >>> Thank you so much,
>              >>>
>              >>> Casandra
>              >>>
>              >>> _______________________________________________
>              >>> Bioperl-l mailing list
>              >>> [hidden email]
>             <mailto:[hidden email]>
>              >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>              >>
>              >>
>              >>
>              >>
>              >
>              > _______________________________________________
>              > Bioperl-l mailing list
>              > [hidden email]
>             <mailto:[hidden email]>
>              > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>             --
>             ------------------------------------------------------------------------
>             Scott Cain, Ph. D. scott at scottcain dot net
>             GMOD Coordinator (http://gmod.org/) 216-392-3087
>             <tel:216-392-3087>
>             Ontario Institute for Cancer Research
>
>             _______________________________________________
>             Bioperl-l mailing list
>             [hidden email]
>             <mailto:[hidden email]>
>             http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
>
>     --
>     Casandra Riera
>     +34 629774181 <tel:%2B34%20629774181>
>     Barcelona, Spain.
>
>     [hidden email] <mailto:[hidden email]>
>     http://terrainsalo.blogspot.com/
>
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Dave Messina-3
Ah right, that's a good point. Well, don't I feel like the asshole. :)

Once local::lib and cpanm are installed, it's possible to run cpanm on the
tarball downloaded from github, right?

i.e.
cpanm bioperl-live-bioperl-release-**1-5-1-rc4-4318-g342e587.zip

And that should take care of dependencies, then, correct?


either by simply documenting this or by getting a script up and running for
> them.  This will resolve down-stream problems (for instance, if the
> distribution is split up).


Agreed, that's a great idea.


Best,
Dave




On Tue, Feb 7, 2012 at 23:50, Chris Fields <[hidden email]> wrote:

> The catch with a PERL5LIB approach for a new installation is the very
> possibility that non-core dependencies will not be installed.  We'll have
> a response down the road for 'why did Bio::Foo fail with the following
> error', with an obvious missing dependency being the problem.
>
> We've been discussing this on IRC (scott, leont and I). I tend to think
> the best solution for new users is to set them up with both local::lib and
> cpanm initially, either by simply documenting this or by getting a script
> up and running for them.  This will resolve down-stream problems (for
> instance, if the distribution is split up).
>
> chris
>
>
>
> On 02/07/2012 04:39 PM, Dave Messina wrote:
>
>> Hi Casandra,
>>
>> (Wayne already answered this much more succinctly than me, but here is
>> my answer anyway.)
>>
>>
>> I think you're almost there.
>>
>> The fact that you get no error message when you type
>> perl -e "use Bio::SeqIO;"
>>
>> in the directory src/bioperl-live/ tells me that probably Perl doesn't
>> "see" where you put BioPerl. That's what the PERL5LIB variable does; it
>> tells Perl that it should look for Perl modules in the directories named
>> in the environmental variable PERL5LIB.
>>
>> If you type
>>
>> printenv PERL5LIB
>>
>> do you see
>>
>> /Users/mcasandrariera/src/**bioperl-live
>>
>> ?
>>
>> If not, then redo steps 5-10 and then try typing
>> printenv PERL5LIB
>>
>> again. Make sure that in step 8, instead of
>>
>> export PERL5LIB=/Users/dave/src/**bioperl-live
>>
>> you type
>>
>> export PERL5LIB=/Users/**mcasandrariera/src/bioperl-**live
>>
>>
>> To answer your other questions:
>>
>>    although I don't know what src means...
>>
>>
>> src is just a directory name. It's short for "source", which itself is
>> really short for "source code". src the name of the directory where I
>> keep all of my source code libraries like BioPerl.
>>
>>
>>    Maybe it will be useless to explain it to me, but, why this method
>>    isn't "installing" Bioperl? Why I didn't need to do all those
>>    preliminary steps, use Fink, and so on? I mean, if I can finally do
>>    the same (using Bioperl).
>>
>>
>> The short answer is that by following the zero-install instructions, you
>> won't be able use some parts of BioPerl (which I'm betting you won't
>> need right away).
>>
>> Chris and Scott's advice is correct and the right way to go in the long
>> run. Once you've gotten your feet wet a bit and become more familiar
>> with Perl and BioPerl, you may want to come back to their approach and
>> try it again.
>>
>>
>> Best,
>> Dave
>>
>>
>>
>>
>>
>> On Tue, Feb 7, 2012 at 23:05, casandra <[hidden email]
>> <mailto:mcasandrariera@gmail.**com <[hidden email]>>> wrote:
>>
>>    Ok, this is what happened. I guess this mean it worked, didn't it?
>>
>>    Last login: Tue Feb 7 22:47:16 on ttys000
>>    maccasandra:~ mcasandrariera$ perl -e "use Bio::SeqIO;"
>>    Can't locate Bio/SeqIO.pm in @INC (@INC contains:
>>    /Users/mcasaandrariera/src/**bioperl-live
>>    /Library/Perl/5.12/darwin-**thread-multi-2level /Library/Perl/5.12
>>    /Network/Library/Perl/5.12/**darwin-thread-multi-2level
>>    /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3
>>    /System/Library/Perl/5.12/**darwin-thread-multi-2level
>>    /System/Library/Perl/5.12
>>    /System/Library/Perl/Extras/5.**12/darwin-thread-multi-2level
>>    /System/Library/Perl/Extras/5.**12 .) at -e line 1.
>>    BEGIN failed--compilation aborted at -e line 1.
>>    maccasandra:~ mcasandrariera$ cd ./src/bioperl-live/
>>    maccasandra:bioperl-live mcasandrariera$ perl -e "use Bio::SeqIO;"
>>    maccasandra:bioperl-live mcasandrariera$
>>
>>    I took your src name (I hadn't any better suggestion, although I
>>    don't know what src means... :P)
>>
>>    Thank you so much to all of you! I have to say that it was a big
>>    relief reading Dave telling so simple things :D thanks!
>>
>>    Maybe it will be useless to explain it to me, but, why this method
>>    isn't "installing" Bioperl? Why I didn't need to do all those
>>    preliminary steps, use Fink, and so on? I mean, if I can finally do
>>    the same (using Bioperl).
>>
>>    And related to the previous method I tried, I read that you were
>>    discussing "that she wants to use local::lib, but there need to be
>>    some prereqs installed, but they can't be because she chose to use
>>    local::lib, and it's not installed. " I really didn't "wanted" to
>>    use it, I chose it because it was the default option, and, since I
>>    didn't know about the alternatives, I thought that the default would
>>    be ok... But if what Dave said works, better for me, I didn't really
>>    know what I was doing with thosesteps (but I want to learn it soon! ;)
>> )
>>
>>    Thank you all for your time ;)
>>
>>    Casandra
>>
>>    El 7 de febrero de 2012 22:38, Dave Messina <[hidden email]
>>    <mailto:[hidden email].**se <[hidden email]>>>
>> escribió:
>>
>>
>>        I will take the opportunity to shamelessly pimp my no-install
>>        install instructions (below and
>>        http://seqxml.org/xml/BioPerl.**html<http://seqxml.org/xml/BioPerl.html>).
>> IMHO if Casandra is just
>>        looking to get started with BioPerl, messing with external libs
>>        and configs is probably overkill.
>>
>>        Best,
>>        Dave
>>
>>
>>
>>        There’s a quickie, “zero-install” way to get BioPerl on your
>> system.
>>        1) Okay, click here to download bioperl as a zip file:
>>
>>        https://github.com/bioperl/**bioperl-live/zipball/master<https://github.com/bioperl/bioperl-live/zipball/master>
>>
>>
>>        when it's done downloading, unzip it if your computer hasn’t
>>        done it automatically. On the
>>        command line, you would do:
>>
>>        unzip bioperl-live-bioperl-release-**1-5-1-rc4-4318-g342e587.zip
>>
>>        or whatever the file is called. You should then have a folder
>>        with some ugly name like
>>
>>        bioperl-bioperl-live-558467a
>>
>>        3) rename that to
>>
>>        bioperl-live
>>
>>        4) move that folder to wherever you want to keep it. I keep mine
>>        in a directory called src in my
>>        home directory.
>>
>>        So on my computer if I go to the command line and cd to that
>>        folder and type pwd I get:
>>
>>        /Users/dave/src/bioperl-live
>>
>>        5) in the terminal, cd to your home directory.
>>
>>        6) see if you have a file named .bash_profile by typing
>>
>>        ls -l ~/.bash_profile
>>
>>        7) if so, open that file in your favorite editor. if the file
>>        doesn't exist, just create the file.
>>
>>        8) put this line in your .bash_profile
>>
>>        export PERL5LIB=/Users/dave/src/**bioperl-live
>>
>>        (obviously replacing my path info with wherever you chose to put
>>        bioperl)
>>
>>        9) save and close your .bash_profile
>>
>>        10) open a new terminal window so that the change will take effect.
>>
>>        11) on the command line of the new terminal, type
>>
>>        perl -e "use Bio::SeqIO;"
>>
>>        If that works, then you have "installed" bioperl. Yay!
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>        On Tue, Feb 7, 2012 at 22:12, Scott Cain <[hidden email]
>>        <mailto:[hidden email]>> wrote:
>>
>>            Yes, but those doc don't address exactly the problem
>>            Cassandra is
>>            having, that she wants to use local::lib, but there need to
>>            be some
>>            prereqs installed, but they can't be because she chose to use
>>            local::lib, and it's not installed. That's all fine if
>>            you're not a
>>            newbie and know how to properly install the prereqs before
>>            using the
>>            cpan shell, but when following instructions that say "use
>>            local::lib",
>>            I find that the instructions are completely insufficient in
>>            actually
>>            getting the desired software installed. Thus the need for a
>> good
>>            tutorial.
>>
>>            Scott
>>
>>
>>            On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields
>>            <[hidden email] <mailto:[hidden email]>**>
>> wrote:
>>             > I guess one key question is where these CPAN installation
>>            instructions come
>>             > from. They're a bit odd, and if this is from the wiki we
>>            need to do some
>>             > updating.
>>             >
>>             > Re: local::lib, the docs on CPAN are pretty nice if one
>>            wants to use a
>>             > single perl version.
>>             >
>>             >
>>            https://metacpan.org/module/**local::lib#The-bootstrapping-**
>> technique<https://metacpan.org/module/local::lib#The-bootstrapping-technique>
>>             >
>>             > In my case I use perlbrew (which is all local by default,
>>            and allows
>>             > switching between perl versions). Highly recommend using
>>            either simple
>>             > local::lib or perlbrew in combination with cpanm.
>>             >
>>             > https://metacpan.org/module/**perlbrew<https://metacpan.org/module/perlbrew>
>>             > https://metacpan.org/module/**cpanm<https://metacpan.org/module/cpanm>
>>             >
>>             > chris
>>
>>             >
>>             >
>>             >
>>             > On 02/07/2012 02:55 PM, Scott Cain wrote:
>>             >>
>>             >> hi Cassandra,
>>             >>
>>             >> I don't have an answer for you at the moment. It seems
>>            to me that
>>             >> using local::lib is a good idea, but I've never found a
>>            good tutorial
>>             >> for using it, so I haven't. Perhaps someone else on the
>>            list can
>>             >> suggest one.
>>             >>
>>             >> The other thing I just wanted to mention as the admin
>>            that approved
>>             >> your message--I came very close to deleting it from the
>>            queue without
>>             >> looking at it because it is not unusual for spam
>>            messages to have
>>             >> generic subjects like "help!" (just for future reference
>> :-)
>>             >>
>>             >> Scott
>>             >>
>>             >>
>>             >> On Tue, Feb 7, 2012 at 11:11 AM,
>>            Casandra<[hidden email] <mailto:[hidden email]>>
>>
>>            wrote:
>>             >>>
>>             >>> Hi,
>>             >>>
>>             >>> I'm trying to install Bioperl but I'm a bit lost. I
>>            know I have perl
>>             >>> installed becaused I have already write some scripts
>>            but I'm biologist
>>             >>> so...
>>             >>> not pretty sure about what messages say.
>>             >>>
>>             >>> My perl version:
>>             >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
>>             >>> My computer:
>>             >>> Mac OS X Vesion 10.5.8
>>             >>>
>>             >>> I was following this preliminary steps:
>>             >>>
>>             >>> --------------
>>             >>>
>>             >>> PRELIMINARY PREPARATION
>>             >>>
>>             >>> This is optional, but regardless of your subsequent
>>            choice of
>>             >>> installation method, it will help to carry out the
>>            following steps.
>>             >>> They will increase the likelyhood of installation success
>>             >>> (especially of optional dependencies).
>>             >>>
>>             >>> * Upgrade CPAN:
>>             >>>
>>             >>> >perl -MCPAN -e shell
>>             >>> cpan>install Bundle::CPAN
>>             >>> cpan>q
>>             >>>
>>             >>> * Install/upgrade Module::Build, and make it your
>> preferred
>>             >>> installer:
>>             >>>
>>             >>> >cpan
>>             >>> cpan>install Module::Build
>>             >>> cpan>o conf prefer_installer MB
>>             >>> cpan>o conf commit
>>             >>> cpan>q
>>             >>>
>>             >>> * Install the expat library by whatever method is
>>             >>> appropriate for your system.
>>             >>>
>>             >>> * If your expat library is installed in a non-standard
>>            location,
>>             >>> tell CPAN about it:
>>             >>>
>>             >>> >cpan
>>             >>> cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/**lib
>>             >>> EXPATINCPATH=/non-standard/**include"
>>             >>> cpan>o conf commit
>>             >>>
>>             >>> --------------
>>             >>>
>>             >>> And I think I did "Upgrade CPAN properly" but when I
>>            tried the next one
>>             >>> it
>>             >>> started asking too many things to me, and finally it
>>            stopped due to "some
>>             >>> problems". In text file you can see the whole process.
>>             >>> What did I do wrong?
>>             >>>
>>             >>>
>>             >>> After solving these preliminary steps, what should I
>>            do? What exactly
>>             >>> .tar
>>             >>> or .whatever should I download to install?
>>             >>>
>>             >>> I don't see the difference between installing it
>>            through "built.PL" or
>>             >>> CPAN. And I don't know if I should do this or that
>>            "Fink*" stuff for
>>             >>> MAC.
>>             >>>
>>             >>> * I went to Fink webpage and what I expected to see was
>>            "hello! download
>>             >>> Bioperl simply clicking here!" but far from this, what
>>            it seems is that
>>             >>> first I have to download some kinf of Fink-program
>>            before starting with
>>             >>> Bioperl... is it something close to this?
>>             >>>
>>             >>> I'm sorry, too many questions... But I really want to
>>            learn to use
>>             >>> Bioperl
>>             >>> but I have no people to ask it face to face.
>>             >>>
>>             >>> Thank you so much,
>>             >>>
>>             >>> Casandra
>>             >>>
>>             >>> ______________________________**_________________
>>             >>> Bioperl-l mailing list
>>             >>> [hidden email]
>>            <mailto:[hidden email]-**bio.org<[hidden email]>
>> >
>>
>>             >>> http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>             >>
>>             >>
>>             >>
>>             >>
>>             >
>>             > ______________________________**_________________
>>             > Bioperl-l mailing list
>>             > [hidden email]
>>            <mailto:[hidden email]-**bio.org<[hidden email]>
>> >
>>
>>             > http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>
>>
>>
>>            --
>>            ------------------------------**------------------------------
>> **------------
>>            Scott Cain, Ph. D. scott at scottcain dot net
>>            GMOD Coordinator (http://gmod.org/) 216-392-3087
>>            <tel:216-392-3087>
>>
>>            Ontario Institute for Cancer Research
>>
>>            ______________________________**_________________
>>            Bioperl-l mailing list
>>            [hidden email]
>>            <mailto:[hidden email]-**bio.org<[hidden email]>
>> >
>>
>>            http://lists.open-bio.org/**mailman/listinfo/bioperl-l<http://lists.open-bio.org/mailman/listinfo/bioperl-l>
>>
>>
>>
>>
>>
>>    --
>>    Casandra Riera
>>    +34 629774181 <tel:%2B34%20629774181>
>>    Barcelona, Spain.
>>
>>    [hidden email] <mailto:mcasandrariera@gmail.**com<[hidden email]>
>> >
>>    http://terrainsalo.blogspot.**com/ <http://terrainsalo.blogspot.com/>
>>
>>
>>
>

_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Fields, Christopher J
On Feb 7, 2012, at 5:33 PM, Dave Messina wrote:

> Ah right, that's a good point. Well, don't I feel like the asshole. :)

Nah.  It's something we've done for quite a while, but we probably should adopt something that works better in the long run.

> Once local::lib and cpanm are installed, it's possible to run cpanm on the tarball downloaded from github, right?
>
> i.e.
> cpanm bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
>
> And that should take care of dependencies, then, correct?

Yep.  One can install from a URL as well:

cpanm http://example.org/LDS/CGI.pm-3.20.tar.gz

> either by simply documenting this or by getting a script up and running for them.  This will resolve down-stream problems (for instance, if the distribution is split up).
>
> Agreed, that's a great idea.
>
>
> Best,
> Dave

chris
_______________________________________________
Bioperl-l mailing list
[hidden email]
http://lists.open-bio.org/mailman/listinfo/bioperl-l
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: help!

Fields, Christopher J
In reply to this post by Dave Messina-3
All,

The master branch on github is undergoing significant changes that will break your code; in short, it is missing several modules that were removed due to our work on modularization.  If you really need to grab the latest stable code, I recommend either getting the latest CPAN release (v1.6.924, just released a month ago) or using the ‘v1.6.x’ branch on GitHub, which we have been routinely patching with fixes to the main branch.

If needed we can switch the default checkout branch to ‘v1.6.x' to make things easier (so far there has been no consensus about this, so I am leaving it as is for the time being).

chris

On Aug 1, 2014, at 1:20 PM, Tess Cherlin <[hidden email]> wrote:

Hi Dave, Chris, Cassandra and others,

I was following the wonderful directions that Dave wrote and have made it to an almost similar end as Cassandra.


ncfa-2-3502-ap3:~ Vi$ perl -e "use Bio::SeqIO;"
Base class package "Bio::Root::Root" is empty.
    (Perhaps you need to 'use' the module which defines that package first.)
 at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/WidestCoordPolicy.pm line 80.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Atomic.pm line 79.
Compilation failed in require at (eval 1) line 3.
    ...propagated at /System/Library/Perl/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Location/Simple.pm line 87.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/Factory/FTLocationFactory.pm line 97.
Compilation failed in require at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
BEGIN failed--compilation aborted at /Users/Vi/bioperl-live/Bio/SeqIO.pm line 330.
Compilation failed in require at -e line 1.
BEGIN failed--compilation aborted at -e line 1.
ncfa-2-3502-ap3:~ Vi$ 


I see that there are many items that were not compiled "aborted", is that something I need to do separately? I'm sorry but I got lost when Dave and Chris began discussing the stuff at the bottom of this chain. So if someone could explain a solution simply I would greatly appreciate it!

Thank you!

Tess

On Tuesday, February 7, 2012 3:38:12 PM UTC-6, Dave Messina wrote:
I will take the opportunity to shamelessly pimp my no-install install
instructions (below and http://seqxml.org/xml/BioPerl.html). IMHO if
Casandra is just looking to get started with BioPerl, messing with external
libs and configs is probably overkill.

Best,
Dave


 There’s a quickie, “zero-install” way to get BioPerl on your system.

    1) Okay, click here to download bioperl as a zip file:

    https://github.com/bioperl/bioperl-live/zipball/master


    when it's done downloading, unzip it if your computer hasn’t done it
automatically. On the
    command line, you would do:

         unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip

    or whatever the file is called. You should then have a folder with some
ugly name like

    bioperl-bioperl-live-558467a

    3) rename that to

    bioperl-live

    4) move that folder to wherever you want to keep it. I keep mine in a
directory called src in my
        home directory.

    So on my computer if I go to the command line and cd to that folder and
type pwd I get:

    /Users/dave/src/bioperl-live

    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't
exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put
bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!







On Tue, Feb 7, 2012 at 22:12, Scott Cain <sc...@scottcain.net> wrote:

> Yes, but those doc don't address exactly the problem Cassandra is
> having, that she wants to use local::lib, but there need to be some
> prereqs installed, but they can't be because she chose to use
> local::lib, and it's not installed.  That's all fine if you're not a
> newbie and know how to properly install the prereqs before using the
> cpan shell, but when following instructions that say "use local::lib",
> I find that the instructions are completely insufficient in actually
> getting the desired software installed.  Thus the need for a good
> tutorial.
>
> Scott
>
>
> On Tue, Feb 7, 2012 at 4:02 PM, Chris Fields <cjfi...@illinois.edu>
> wrote:
> > I guess one key question is where these CPAN installation instructions
> come
> > from.  They're a bit odd, and if this is from the wiki we need to do some
> > updating.
> >
> > Re: local::lib, the docs on CPAN are pretty nice if one wants to use a
> > single perl version.
> >
> > https://metacpan.org/module/local::lib#The-bootstrapping-technique
> >
> > In my case I use perlbrew (which is all local by default, and allows
> > switching between perl versions).  Highly recommend using either simple
> > local::lib or perlbrew in combination with cpanm.
> >
> > https://metacpan.org/module/perlbrew
> > https://metacpan.org/module/cpanm
> >
> > chris
> >
> >
> >
> > On 02/07/2012 02:55 PM, Scott Cain wrote:
> >>
> >> hi Cassandra,
> >>
> >> I don't have an answer for you at the moment.  It seems to me that
> >> using local::lib is a good idea, but I've never found a good tutorial
> >> for using it, so I haven't.  Perhaps someone else on the list can
> >> suggest one.
> >>
> >> The other thing I just wanted to mention as the admin that approved
> >> your message--I came very close to deleting it from the queue without
> >> looking at it because it is not unusual for spam messages to have
> >> generic subjects like "help!"  (just for future reference :-)
> >>
> >> Scott
> >>
> >>
> >> On Tue, Feb 7, 2012 at 11:11 AM, Casandra<kasa...@gmail.com>  wrote:
> >>>
> >>> Hi,
> >>>
> >>> I'm trying to install Bioperl but I'm a bit lost. I know I have perl
> >>> installed becaused I have already write some scripts but I'm biologist
> >>> so...
> >>> not pretty sure about what messages say.
> >>>
> >>> My perl version:
> >>> This is perl, v5.8.8 built for darwin-thread-multi-2level
> >>> My computer:
> >>> Mac OS X Vesion 10.5.8
> >>>
> >>> I was following this preliminary steps:
> >>>
> >>> --------------
> >>>
> >>> PRELIMINARY PREPARATION
> >>>
> >>>    This is optional, but regardless of your subsequent choice of
> >>>    installation method, it will help to carry out the following steps.
> >>>    They will increase the likelyhood of installation success
> >>>    (especially of optional dependencies).
> >>>
> >>>      * Upgrade CPAN:
> >>>
> >>>  >perl -MCPAN -e shell
> >>>  cpan>install Bundle::CPAN
> >>>  cpan>q
> >>>
> >>>      * Install/upgrade Module::Build, and make it your preferred
> >>>        installer:
> >>>
> >>>  >cpan
> >>>  cpan>install Module::Build
> >>>  cpan>o conf prefer_installer MB
> >>>  cpan>o conf commit
> >>>  cpan>q
> >>>
> >>>      * Install the expat library by whatever method is
> >>>        appropriate for your system.
> >>>
> >>>      * If your expat library is installed in a non-standard location,
> >>>        tell CPAN about it:
> >>>
> >>>  >cpan
> >>>  cpan>o conf makepl_arg "EXPATLIBPATH=/non-standard/lib
> >>> EXPATINCPATH=/non-standard/include"
> >>>  cpan>o conf commit
> >>>
> >>> --------------
> >>>
> >>> And I think I did "Upgrade CPAN properly" but when I tried the next one
> >>> it
> >>> started asking too many things to me, and finally it stopped due to
> "some
> >>> problems". In text file you can see the whole process.
> >>> What did I do wrong?
> >>>
> >>>
> >>> After solving these preliminary steps, what should I do? What exactly
> >>> .tar
> >>> or .whatever should I download to install?
> >>>
> >>> I don't see the difference between installing it through "built.PL" or
> >>>  CPAN. And I don't know if I should do this or that "Fink*" stuff for
> >>> MAC.
> >>>
> >>> * I went to Fink webpage and what I expected to see was "hello!
> download
> >>> Bioperl simply clicking here!" but far from this, what it seems is that
> >>> first I have to download some kinf of Fink-program before starting with
> >>> Bioperl... is it something close to this?
> >>>
> >>> I'm sorry, too many questions... But I really want to learn to use
> >>> Bioperl
> >>> but I have no people to ask it face to face.
> >>>
> >>> Thank you so much,
> >>>
> >>> Casandra
> >>>
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Biop...@lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Biop...@lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> _______________________________________________
> Bioperl-l mailing list
> Biop...@lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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



_______________________________________________
Bioperl-l mailing list
[hidden email]
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
Loading...