[BioBrew Users] Biobrew 4.1.1 installation on a running cluster
kannaiah at bsd.uchicago.edu
kannaiah at bsd.uchicago.edu
Fri May 5 11:12:14 EDT 2006
Hello,
Anybody have these kind of errors while installing the rpm packages in Biobrew
4.1.1.
error 1) do i need to worry about the user or group warning here?
error 2) i tried installing the EMBOSS-libs first, but that didnt install at all.
error 3) What does not an rpm package (or package manifest): mean?
error 4) I know i have the regular ncbi-blast(blastall) installed.
gridengine...we have the sge installed, so where is it trying to look
for those packages?
Thanks for all the help:)
----------------------------------
1) rpm -ivh clustalw-1.8.3-1.x86_64.rpm
Preparing... ########################################### [100%]
1:clustalw warning: user gotero does not exist - using root
warning: group gotero does not exist - using root
warning: user gotero does not exist - using root
warning: group gotero does not exist - using root
----------------------------------
2) rpm -ivh EMBOSS-3.0.0-1.x86_64.rpm
error: Failed dependencies:
libajax.so.3()(64bit) is needed by EMBOSS-3.0.0-1.x86_64
libajaxg.so.3()(64bit) is needed by EMBOSS-3.0.0-1.x86_64
libnucleus.so.3()(64bit) is needed by EMBOSS-3.0.0-1.x86_64
libplplot.so.5()(64bit) is needed by EMBOSS-3.0.0-1.x86_64
-----------------------------------
3) rpm -ivh EMBOSS-libs-3.0.0-1.x86_64.rpm
EMBOSS-libs-3.0.0-1.x86_64.rpm: not an rpm package (or package manifest):
-----------------------------------------
4) rpm -ivh sgeblast-0.2-1.x86_64.rpm
error: Failed dependencies:
gridengine is needed by sgeblast-0.2-1.x86_64
ncbi-blast is needed by sgeblast-0.2-1.x86_64
-----------------------------------------
-Kiran
Quoting kannaiah at bsd.uchicago.edu:
> Hello there
>
> I just installed Biobrew 4.1.1 (prev version i had was the 4.1) on our
> cluster
> frontend. I followed the steps below as given in the docs for a installing
> a
> roll on a running system:
> But i still dont see the biobrew packages installed on the frontend. They
> are
> just stored as rpm files. Do i need to restart the frontend?
> I still havent reinstalled the compute nodes, i was waiting to see if they
> installed correctly on the frontend first.
> ----------------
> # cd /tmp
> # wget
>
http://www.rocksclusters.org/ftp-site/pub/rocks/extras/4.1/x86_64/app-trace-4.1-0.x86_64.disk1.iso
> # mount -o loop app-trace-4.1-0.x86_64.disk1.iso /mnt/cdrom
> # cd /home/install
> # rocks-dist --install copyroll
> # umount /mnt/cdrom
> # rocks-dist dist
> ---------------------
>
> Any suggestions?
>
> Thank you
> Kiran Annaiah
> Dept of Human Genetics
> Univ of Chicago
>
> > 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
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> > -------------------------------------------------
> >
> >
> > ------------------------------
> >
> > 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.
> > > -------------------------------------------------
> > > _______________________________________________
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> > > BioBrew-Users at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> > >
> >
> >
> >
> > ------------------------------
> >
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> >
> > End of BioBrew-Users Digest, Vol 12, Issue 1
> > **********************************************
> >
> >
> >
>
>
>
>
>
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