[BioBrew Users] Possible error with 4.1.2 roll

[Anoop Rajendra]

Programs like flex and byacc are build dependencies for a few  
bioinformatics applications. You'll need to have them installed  
before you actually start compilation. it wont matter if they are  
removed from the xml files. The build is going to fail.

If I'm not mistaken these utilities are available on the OS-3 and  
OS-4 roll CDs from Rocks. You can install them and recompile the  
biobrew roll. If the roll is already compiled with these utilities,  
and you're trying to only install and not build the roll, then I'd  
suggest doing a copyroll on the OS-3 and OS-4 roll cds, before  
running the "kroll" command below.

-Anoop

On May 23, 2006, at 12:31 PM, Jeremy Mann wrote:

> Now it errors that it can't find flex so something is wrong with this
> roll, it keeps wanting to use the 4.1.1 non-existant roll.
>
> On 5/23/06, Jeremy Mann <jeremymann at gmail.com> wrote:
>> Me too. All I can do for now is comment out byacc in the three XML
>> files, biobrew.xml, biobrew-compute.xml and biobrew-frontend.xml. I
>> hope nothing important needs it.
>>
>> On 5/23/06, Glen Otero <glen at callident.com> wrote:
>> > Oh crap. More rocks issues. I'm at a loss here. I'm sure there's a
>> > way to make this work, but I don't know it off the top of my head.
>> > You might try reinstalling the new roll now that you've removed
>> > remains of the old one.
>> >
>> > Glen
>> >
>> > On May 23, 2006, at 9:42 AM, Jeremy Mann wrote:
>> >
>> > > I upgraded the roll from 4.1.1 to 4.1.2 as you said yesterday:
>> > >
>> > > 1) insert the biobrew CD in the frontend node
>> > > 2) cd /home/install
>> > > 3) rocks-dist --install copyroll
>> > > 4) rocks-dist dist
>> > > 5) kroll biobrew > /tmp/install-biobrew.sh
>> > > 6) chmod +x /tmp/install-biobrew.sh
>> > > 7) /tmp/install-biobrew.sh
>> > >
>> > > After doing this, I went to rebuild a node and the installer  
>> says it
>> > > can't find byacc-1.9-28. I issued a find command in /home/ 
>> install and
>> > > that version of byacc is in the old 4.1.1 roll. I then went into
>> > > /home/install/rocks-dist/lan/i386/RedHat/RPMS and the symlink and
>> > > torrent is for byacc-1.9-29.
>> > >
>> > > I was curious if I had to manually remove the 4.1.1 directory and
>> > > issue another rocks-dist dist to update the changes. Now that  
>> I've
>> > > already done that, the installer still wants to install the older
>> > > BioBrew roll.
>> > >
>> > > On 5/23/06, Glen Otero <glen at callident.com> wrote:
>> > >> Jeremy-
>> > >>
>> > >> I'm not sure what's going on here. Can you explain what  
>> you're doing
>> > >> in more detail? What do you mean by deleting the directory and
>> > >> rebuilding with rocks-dist?
>> > >>
>> > >> Glen
>> > >>
>> > >>
>> > >> On May 23, 2006, at 7:07 AM, Jeremy Mann wrote:
>> > >>
>> > >> > I've upgraded our BioBrew roll from 4.1.1 to 4.1.2  
>> following the
>> > >> > instructions from Glen Otero. When rebuilding an i386 node the
>> > >> > installer errors on byacc. It says it cannot find  
>> byacc-1.9.28. The
>> > >> > 4.1.2 roll has byacc-1.9.29. I still have the 4.1.1 roll,  
>> should I
>> > >> > delete that directory and rebuild with rocks-dist to fix this?
>> > >> >
>> > >> > --
>> > >> > Jeremy
>> > >> > _______________________________________________
>> > >> > BioBrew-Users mailing list
>> > >> > BioBrew-Users at bioinformatics.org
>> > >> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>> > >> >
>> > >> >
>> > >>
>> > >> _______________________________________________
>> > >> BioBrew-Users mailing list
>> > >> BioBrew-Users at bioinformatics.org
>> > >> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>> > >>
>> > >
>> > >
>> > > --
>> > > Jeremy
>> > > _______________________________________________
>> > > BioBrew-Users mailing list
>> > > BioBrew-Users at bioinformatics.org
>> > > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>> > >
>> > >
>> >
>> > _______________________________________________
>> > BioBrew-Users mailing list
>> > BioBrew-Users at bioinformatics.org
>> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>> >
>>
>>
>> --
>> Jeremy
>>
>
>
> -- 
> Jeremy
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