[BioBrew Users] Biobrew 4.1.1 installation on a running cluster
kannaiah at bsd.uchicago.edu
kannaiah at bsd.uchicago.edu
Fri May 5 18:55:58 EDT 2006
Thank you, i will try installing the srpms.
We have Redhat AS v4.0 installed.
Quoting Glen Otero <glen at callident.com>:
> What Linux version and release are you using?
>
> Don't worry about error #1.
> Error 2 is worrisome. You might try downloading the SRPM from the
> biobrew website and rebuilding it yourself. You can find it here:
> ftp://ftp.bioinformatics.org/pub/biobrew/srpms/4.1
>
> Unless you're going to use sgeblast, don't worry about the sgeblast
> errors.
>
> I'll try to look into the EMBOSS errors.
>
> Glen
>
> On May 5, 2006, at 8:12 AM, kannaiah at bsd.uchicago.edu wrote:
>
> > 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
> >>> 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.
> >> -------------------------------------------------
> >> _______________________________________________
> >> BioBrew-Users mailing list
> >> BioBrew-Users at bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >>
> >>
> >>
> >
> >
> >
> >
> >
> > -------------------------------------------------
> > 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
>
>
>
-------------------------------------------------
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.
-------------------------------------------------
More information about the BioBrew-Users
mailing list