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 >