[BioBrew Users] Biobrew 4.1.1 installation on a running cluster

Fri May 5 18:26:56 EDT 2006

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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------
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>>> entity to
>>> which
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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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>> 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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>>>>
>>>
>>>
>>>
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>>>
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>>> End of BioBrew-Users Digest, Vol 12, Issue 1
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>>>
>>>
>>>
>>
>>
>>
>>
>>
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>
>
>
>
>
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