[Bioperl-l] bioperl installation

[Jason Stajich]

So you didn't install staden's io_lib...

Before you go any further.  Do you really want to do this?  i.e. do you
intend to process abi tracefiles with bioperl?  if not, don't worry about
this. if you want the alignment stuff go into the Bio/Align directory and
do the makefile stuff there.  READ THE README alot of questions/problems are
discussed in there.

If you don't want the in-perl alignment stuff, stop now and forget about
bioperl-ext.

-jason

On Thu, 22 Jul 2004, Xiang Deng wrote:

> Jason,
>
> Thanks for trying that for me.
>
> I already downloaded and installed Inline-0.44 under directory
> "my_bioperl/bioperl-ext-1.4" and staden library io_lib-1.8.12 under
> directory "my_bioperl/".
> but I still have following errors when installing bioperl-ext-1.4
>
>
> mendel 297% perl Makefile.PL
> LIB=/v0/users/deng0007/my_bioperl/bioperl-ext-1.4
> Writing Makefile for Bio::Ext::Align
> Warning: prerequisite Bio::SeqIO::abi 0 not found.
> Please tell us where your Staden io_lib "read" library is installed:
> [/usr/local/lib] [/v0/users/deng0007/my_bioperl]
> Please tell us where your Staden io_lib "Read.h" header is installed:
> [[/v0/users/deng0007/my_bioperl]/io_lib] [/v0/users/deng0007/my_bioperl]
> Writing Makefile for Bio::SeqIO::staden::read
> Writing Makefile for Bio
> mendel 298% make
>
>
>         DEFINE='-DPOSIX -DNOERROR'; CC='cc -n32'; export DEFINE INC CC; \
>         cd libs && make CC=cc -n32 libsw.a -e
> Usage: make [-f makefile] [-p] [-i] [-k] [-s] [-r] [-n] [-u]
>         [-d] [-D] [-S] [-g] [-w] [-P] [-B] [-b] [-O] [-e] [-t] [-q] [-M]
> [-N] [names]
> *** Error code 1 (bu21)
> *** Error code 1 (bu21)
>
> Do you know what is the problem here? I just followed the install
> instruction, do I miss any parameters there?
>
> thanks,
>
> Xiang
>
> Department of Pharmacology and Cancer Biology
> Duke University Medical Center
> Durham, NC 27710
> Phone: 919-4792339
>
>
>
>
> Jason Stajich <jason at cgt.duhs.duke.edu>
> 07/22/2004 02:38 PM
>
> To
> Xiang Deng <xiang.deng at duke.edu>
> cc
> Bioperl <bioperl-l at bioperl.org>
> Subject
> RE: [Bioperl-l] bioperl installation
>
>
>
>
>
>
> Someone has already setup CPAN on the machine - you need to coordinate
> with the sysadmin or else download the modules by hand and do the install
> manualy.
>
> for each module (Inline::C, et)
> % perl Makefile.PL LIB=~/lib/perl
> % make
> % make install
>
> I have logged into mendel and had the same problems, but I don't have time
> to figure out the best workaround for you other than downloading the
> modules by hand for now or else getting the admin to install these for
> you.
>
>  -jason
>
>  On Thu, 22 Jul 2004, Xiang Deng wrote:
>
> > Brian,
> >
> > I tried that, but I could not enter CPAN shell,
> >
> > mendel 215% perl -e shell -MCPAN
> >
> >
> > Your configuration suggests that CPAN.pm should use a working
> > directory of
> >     /.cpan
> > Unfortunately we could not create the lock file
> >     /.cpan/.lock
> > due to permission problems.
> >
> > Please make sure that the configuration variable
> >     $CPAN::Config->{cpan_home}
> > points to a directory where you can write a .lock file. You can set
> > this variable in either
> >     /usr/local/lib/perl5/5.6.1/CPAN/Config.pm
> > or
> >     /v0/users/deng0007/.cpan/CPAN/MyConfig.pm
> >
> > Could not open >/.cpan/.lock: Permission denied
> >
> > Do I need to create all of those ".cpan/CPAN/MyConfig.pm"? I do not even
> > have the .cpan directory.
> >
> > thanks
> >
> > Xiang
> >
> > Department of Pharmacology and Cancer Biology
> > Duke University Medical Center
> > Durham, NC 27710
> > Phone: 919-4792339
> >
> >
> >
> >
> > "Brian Osborne" <brian_osborne at cognia.com>
> > Sent by: bioperl-l-bounces at portal.open-bio.org
> > 07/22/2004 12:01 PM
> >
> > To
> > "Xiang Deng" <xiang.deng at duke.edu>, "Jason Stajich"
> > <jason at cgt.duhs.duke.edu>
> > cc
> > bioperl-l-bounces at portal.open-bio.org, bioperl-l at bioperl.org
> > Subject
> > RE: [Bioperl-l] bioperl installation
> >
> >
> >
> >
> >
> >
> > Xiang,
> >
> > The section in the on-line instruction, the INSTALL page, talking about
> > installing in a personal area using CPAN is called "INSTALLING BIOPERL
> IN
> > A
> > PERSONAL MODULE AREA":
> >
> > You can also use CPAN to install accessory modules in your
> > local directory. First enter the CPAN shell, then set the
> > arguments for the command "perl Makefile.PL", like this:
> >
> > >perl -e shell -MCPAN
> > cpan>o conf makepl_arg LIB=/home/users/dag/My_Local_Perl_Modules
> >
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org
> > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Xiang Deng
> > Sent: Thursday, July 22, 2004 11:42 AM
> > To: Jason Stajich
> > Cc: bioperl-l-bounces at portal.open-bio.org; bioperl-l at bioperl.org
> > Subject: Re: [Bioperl-l] bioperl installation
> >
> > Thanks for your message, Jason.
> >
> > The problem is I don't have permission to install bioperl into the
> > standard site_perl/system area. From the on-line instruction at
> > bioperl.org the only way I can get it installed is to use "make", not
> > CPAN.
> >
> > So could you please let me know where I can download Inline::MakeMaker
> and
> > Inline::C module. Everything I downloaded is from bioperl.org. I did not
> > see where I can get these two. And if I get it which directory I should
> > put them in.
> >
> > thanks,
> >
> > Xiang
> >
> > Department of Pharmacology and Cancer Biology
> > Duke University Medical Center
> > Durham, NC 27710
> > Phone: 919-4792339
> >
> >
> >
> >
> > Jason Stajich <jason at cgt.duhs.duke.edu>
> > Sent by: bioperl-l-bounces at portal.open-bio.org
> > 07/22/2004 11:25 AM
> >
> > To
> > Xiang Deng <xiang.deng at duke.edu>
> > cc
> > bioperl-l at bioperl.org
> > Subject
> > Re: [Bioperl-l] bioperl installation
> >
> >
> >
> >
> >
> >
> >
> > Did you install Inline::C?
> > >From the README in bioperl-ext directory
> >   o Installing
> >
> >  Depending on your choise of extensions, you might need
> >  Inline::MakeMaker and Inline::C to create the makefile. Use for
> >  example the cpan program to install Inline::MakeMaker and answer yes
> >  when prompted to install Inline::C.
> >
> > This line gives you a hint:
> > > Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
> >
> > Did you also install the staden library?
> > -jason
> > On Thu, 22 Jul 2004, Xiang Deng wrote:
> >
> > > To whom it may concern,
> > >
> > > I am trying to install bioperl locally under my peronal folder. The
> core
> > > modules were successfully installed. I ran through a simple perl
> script
> > to
> > > use bio::perl or bio::seq without complain. but I got problem with
> > > installing bioperl-ext-1.4.
> > >
> > > When I installed core modules I used this
> > > >perl Makefile.PL LIB=/my_local_directory/
> > >
> > > My first question is whether or not I have to use the same way to deal
> > > with ext modules too and I can use the same directory or a separate
> one.
> > >
> > > Actually I tried both and both failed with error message as follows:
> > >
> > > mendel 207% perl Makefile.PL
> > > Checking if your kit is complete...
> > > Looks good
> > > Writing Makefile for Bio::Ext::Align
> > > ERROR from evaluation of
> > >
> >
> /v0/users/deng0007/my_bioperl/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL:
> > > Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
> > > /usr/local/lib/perl5/5.6.1/IP27-irix /usr/local/lib/perl5/5.6.1
> > > /usr/local/lib/perl5/site_perl/5.6.1/IP27-irix
> > > /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl
> > > /v0/users/deng0007/my_bioperl/bioperl-ext-1.4 .) at ./Makefile.PL line
> > 1.
> > > BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> > >
> > > could you please let me know what I did wrong or miss in there? thanks
> a
> > > lot,
> > >
> > > Xiang
> > >
> > > Department of Pharmacology and Cancer Biology
> > > Duke University Medical Center
> > > Durham, NC 27710
> > > Phone: 919-4792339
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu