[buster-discuss] changing @INC for buster

[Kevin Jude]

Thanks for reply, Clemens. Indeed, Buster was looking to the wrong perl
binary. Everything is working much better now.

Best wishes
Kevin

On Wed, Feb 15, 2017 at 11:39 PM, Clemens Vonrhein <
vonrhein at globalphasing.com> wrote:

> Hi Kevin,
>
> this looks like a mismatch between the machine BUSTER was installed on
> and the machine you are running it from. Or did you install BUSTER on
> the same machine you are running it from?
>
> Can you check what
>
>   hostname -s
>   uname
>   which perl
>
>   ls -la $BDG_home/machines
>   grep BDG_perl= $BDG_home/machines/*/host.setup
>
> gives you - and does it point to the correct perl binary on that
> particular host? BUSTER itself is not setting @INC, so it seems like
> that host is getting the wrong perl binary.
>
> Some background:
>
>  * BUSTER picks up the perl location from
>
>     $BDG_home/machines/<HOSTNAME>/host.setup
>
>    where <HOSTNAME> is set to 'hostname -s' output during installation
>    - so pointing to the machine name of the installation host.
>
>  * Now in principle every machine you want to run BUSTER on should be
>    configured afresh using the 'newmachine' administrator command,
>    which would create a new <HOSTNAME> entry under the
>    $BDG_home/machines directory.
>
>  * However, we provide a fallback for any Linux host via
>    $BDG_home/machines/.Linux - which is a symbolic link to the
>    installation host subdirectory.
>
> So if the installation host differs significantly from the machine you
> want to run BUSTER on, this will cause problems. In a heterogeneous
> environment you would run
>
>   cd /where/ever/buster
>   . ./setup-admin.sh
>   adm/bin/newmachine BUSTER `hostname -s`
>
> on each machine you want to run BUSTER on (or a representative of each
> OS/distro/setup you are using in your lab - and using symbolic links
> for all other host of the same kind). This way you ensure that the
> correct settings are fetched out of a central BUSTER installation even
> for different hosts.
>
> What you want is that any host can either fetch
>
>   $BDG_home/machines/`hostname -s`/host.setup
>
> or (if that file doesn't exist)
>
>   $BDG_home/machines/.`uname`/host.setup
>
> How you achieve that depends on your setup: separate installation for
> differnet Linux distros/systems, running 'newmachine' for each host,
> running 'newmachine' for a representativ and then use symbolic links,
> ...
>
> Does that help? Or maybe it is something else entirely - in which case
> the output of the commands above might give us a clue.
>
> Cheers
>
> Clemens, Gerard & Andrew
>
> On Wed, Feb 15, 2017 at 10:24:00AM -0800, Kevin Jude wrote:
> > I just tried to run buster on a new machine and got this error:
> >
> > Can't locate Env.pm in @INC (@INC contains: /opt/my_perl/lib
> > /usr/local/lib64/perl5 /usr/local/share/perl5
> > /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl
> > /usr/lib64/perl5 /usr/share/perl5 .)
> > at /programs/x86_64-linux/buster/20160324/bin/buster/addBfrg line 6.
> > BEGIN failed--compilation aborted at
> > /programs/x86_64-linux/buster/20160324/bin/buster/addBfrg line 6.
> >
> >  *# error in script $BDG_com/addBfrg*
> >
> >   Program stopped.
> >
> > My @INC path is different from where buster is searching, though:
> > [kjude at garcialab-b171-server ~]$ perl -e 'print  "@INC"'
> > /opt/my_perl/lib
> > /programs/x86_64-linux/perl/5.18.2/lib/site_perl/5.18.2/x86_
> 64-linux-thread-multi
> > /programs/x86_64-linux/perl/5.18.2/lib/site_perl/5.18.2
> > /programs/x86_64-linux/perl/5.18.2/lib/5.18.2/x86_64-linux-thread-multi
> > /programs/x86_64-linux/perl/5.18.2/lib/5.18.2 .
> >
> > And Env is in that path
> > (/programs/x86_64-linux/perl/5.18.2/lib/5.18.2/Env.pm).  So how can I
> > get buster to look in the right place? Any advice will be appreciated.
> >
> > --
> > Kevin Jude, PhD
> > Research Specialist, Garcia Lab
> > Departments of Molecular & Cellular Physiology and Structural Biology
> > Stanford University School of Medicine
> > Beckman B177, 279 Campus Drive, Stanford CA 94305
> > Phone: (650) 723-6431
>



-- 
Kevin Jude, PhD
Research Specialist, Garcia Lab
Departments of Molecular & Cellular Physiology and Structural Biology
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
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