[BioBrew Users] mpiblast and other biobrew apps

[kannaiah at bsd.uchicago.edu]

Hello,

So, i tried manually installing the rpm package of mpiblast. Did a 
"rpm -i --force --nodeps mpiblast*.rpm"  from the frontend.
I was able run mpiblast from frontend after that. 

But to install on the compute node, i reinstalled the compute node by doing
"/boot/kickstart/cluster-kickstart", but didnt work.

I also noticed that the rpm file is in 3 different directory paths. Whats the
purpose of that? The one i installed was under /home/install.

/export/home/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
/root/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
/share/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm

Thank you
Kiran

> 
> Today's Topics:
> 
>    1. mpiblast and other biobrew apps (kannaiah at bsd.uchicago.edu)
>    2. Re: mpiblast and other biobrew apps (Glen Otero)
> 
> .
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon,  1 May 2006 09:13:30 -0500
> From: kannaiah at bsd.uchicago.edu
> Subject: [BioBrew Users] mpiblast and other biobrew apps
> To: BioBrew-Users at bioinformatics.org
> Message-ID: <1146492810.4456178af3177 at netmail.bsd.uchicago.edu>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hello,
> 
> We installed Biobrew roll on our Rocks cluster. But i dont see any of the
> Biobrew apps having installed on the cluster. I only see their rpms sitting
> in
> certain folders. I checked on mpiblast and this is what i found (output of
> FIND
> command)
> 
>
/home/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>
/home/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm.torrent
> /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>
/share/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
>
/share/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm.torrent
> /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
> 
> Do i need to manually install these rpms? Or did the Biobrew not install
> correctly?
> 
> I have not run mpiblast before, but shouldnt i be able to type "mpiblast" on
> the
> command line?
> Likewise Hmmer and other packages of Biobrew.
> 
> Thanks for the help
> 
> -Kiran
> 
> 
> 
> 
> 
> 
> 
> 
> -------------------------------------------------
> This email is intended only for the use of the individual or entity to
> which
> it is addressed and may contain information that is privileged and
> confidential.  If the reader of this email message is not the intended
> recipient, you are hereby notified that any dissemination, distribution, or
> copying of this communication is prohibited.  If you have received this
> email
> in error, please notify the sender and destroy/delete all copies of the
> transmittal.  Thank you.
> -------------------------------------------------
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 1 May 2006 08:44:09 -0700
> From: Glen Otero <glen at callident.com>
> Subject: Re: [BioBrew Users] mpiblast and other biobrew apps
> To: The Virtual BioBrew Think Tank
> 	<BioBrew-Users at bioinformatics.org>
> Message-ID: <C45059D0-ADA2-4E9C-86E4-DFFA1B694CFB at callident.com>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> 
> Hi Kiran-
> 
> The version of the BioBrew roll you have does have a few problems  
> that prevent the rpms from installing automatically. So you will have  
> to install the rpms yourself. But if you download and install the  
> latest roll, 4.1.1, the rpms should install automatically.
> 
> Glen
> 
> On May 1, 2006, at 7:13 AM, kannaiah at bsd.uchicago.edu wrote:
> 
> > Hello,
> >
> > We installed Biobrew roll on our Rocks cluster. But i dont see any  
> > of the
> > Biobrew apps having installed on the cluster. I only see their rpms  
> > sitting in
> > certain folders. I checked on mpiblast and this is what i found  
> > (output of FIND
> > command)
> >
> > /home/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/ 
> > rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
> > /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> > mpiblast-1.4.0-1.x86_64.rpm.torrent
> > /home/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> > mpiblast-1.4.0-1.x86_64.rpm
> > /share/install/ftp.rocksclusters.org/pub/rocks/rocks-4.1/rocks-dist/ 
> > rolls/biobrew/4.1/x86_64/RedHat/RPMS/mpiblast-1.4.0-1.x86_64.rpm
> > /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> > mpiblast-1.4.0-1.x86_64.rpm.torrent
> > /share/install/rocks-dist/lan/x86_64/RedHat/RPMS/ 
> > mpiblast-1.4.0-1.x86_64.rpm
> >
> > Do i need to manually install these rpms? Or did the Biobrew not  
> > install correctly?
> >
> > I have not run mpiblast before, but shouldnt i be able to type  
> > "mpiblast" on the
> > command line?
> > Likewise Hmmer and other packages of Biobrew.
> >
> > Thanks for the help
> >
> > -Kiran
> >
> >
> >
> >
> >
> >
> >
> >
> > -------------------------------------------------
> > This email is intended only for the use of the individual or entity  
> > to which
> > it is addressed and may contain information that is privileged and
> > confidential.  If the reader of this email message is not the intended
> > recipient, you are hereby notified that any dissemination,  
> > distribution, or
> > copying of this communication is prohibited.  If you have received  
> > this email
> > in error, please notify the sender and destroy/delete all copies of  
> > the
> > transmittal.  Thank you.
> > -------------------------------------------------
> > _______________________________________________
> > 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
> 
> 
> End of BioBrew-Users Digest, Vol 12, Issue 1
> **********************************************
> 
> 
> 





-------------------------------------------------
This email is intended only for the use of the individual or entity to which
it is addressed and may contain information that is privileged and
confidential.  If the reader of this email message is not the intended
recipient, you are hereby notified that any dissemination, distribution, or
copying of this communication is prohibited.  If you have received this email
in error, please notify the sender and destroy/delete all copies of the
transmittal.  Thank you.
-------------------------------------------------