From tony.travis at abdn.ac.uk Sun Nov 3 17:45:24 2013 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sun, 3 Nov 2013 22:45:24 +0000 Subject: [Bio-linux-dev] Problems upgrading Ubuntu 12.04.3 to Bio-Linux 7 Message-ID: <5276D204.6060107@abdn.ac.uk> Hi, Tim. I encountered two problems today when upgrading a recent install of Ubuntu 12.04.3 LTS to Bio-Linux 7 on my server "kitcat". First, the CRAN repository is not added, but is preserved if it is found. Second, there is a conflict between bio-linux-glimmer3 and tigr-glimmer. Here is a quick summary of how I installed Bio-Linux 7: HTH, Tony. > Upgrade "kitcat" to Bio-Linux 7 > # login on "kitcat" and sudo -i > root at kitcat:~# mkdir upgrade > cd upgrade > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > ... > root at kitcat:~/upgrade# tail -20 bl_do_update_to7.log > Building dependency tree... > Reading state information... > Some packages could not be installed. This may mean that you have > requested an impossible situation or if you are using the unstable > distribution that some required packages have not yet been created > or been moved out of Incoming. > The following information may help to resolve the situation: > > The following packages have unmet dependencies. > galaxy-server-all : Depends: r-cran-prettyr but it is not going to be installed > Depends: r-cran-leaps but it is not going to be installed > Depends: r-cran-tcltk2 but it is not going to be installed > Depends: r-cran-rwave but it is not going to be installed > Depends: r-cran-wavethresh but it is not going to be installed > Depends: r-cran-waveslim but it is not going to be installed > Depends: r-cran-bitops but it is not going to be installed > Recommends: ucsc-tools-non-free but it is not installable > Recommends: laj but it is not installable > E: Unable to correct problems, you have held broken packages. > Not all packages installed properly - exiting. > > # add CRAN mirror - preserved, but not added by bl_do_update_to7.sh > vim /etc/apt/sources.list.d/nebc-bio-linux-precise.list > ... > deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ > ... > > # re-run > bl_do_update_to7.sh > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > ... > Reading package lists... > Building dependency tree... > Reading state information... > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > > Verifying that everything installed... > bio-linux-glimmer3 failed to install > Not all packages installed properly - exiting. > > # check package dependencies > apt-cache depends bio-linux-glimmer3 > root at kitcat:~/upgrade# apt-cache depends bio-linux-glimmer3 > bio-linux-glimmer3 > Depends: glimmer3 > Conflicts: > Conflicts: > Replaces: > Replaces: > Replaces: tigr-glimmer > glimmer3 > Replaces: tigr-glimmer:i386 > glimmer3:i386 > > # download > bl_master_package_list.sh > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh > > # remove tigr-glimmer > vim bl_master_package_list.sh > > ... > /tigr-glimmer > dd > :wq > > # edit update script to run bl_master_package_list.sh locally > > vim bl_do_update_to7.sh > > ... > root at kitcat:~/upgrade# diff -Naur bl_do_update_to7.sh bl_do_update_to7.sh.orig > --- bl_do_update_to7.sh 2013-11-03 14:08:25.072271905 +0000 > +++ bl_do_update_to7.sh.orig 2012-12-03 11:54:38.000000000 +0000 > @@ -165,8 +165,7 @@ > # Now the main upgrade - fetch the script and run > # runurl should come from the PPA > apt-get install runurl > -#runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" > -bash bl_master_package_list.sh > +runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" > if [ $? != 0 ] ; then > echo "Not all packages installed properly - exiting." > exit 1 > > # run again with local modified > bl_master_package_list.sh > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. From tbooth at ceh.ac.uk Mon Nov 4 04:58:40 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Nov 2013 09:58:40 +0000 Subject: [Bio-linux-dev] Problems upgrading Ubuntu 12.04.3 to Bio-Linux 7 In-Reply-To: <5276D204.6060107@abdn.ac.uk> References: <5276D204.6060107@abdn.ac.uk> Message-ID: <1383559120.3404.273.camel@balisaur> Hi Tony, Thanks for that. I renamed tigr-glimmer and forgot to change the script, but have fixed it now. With R, when Bio-Linux 7 came out it made sense that you could choose to use either the R from Ubuntu or the latest one from CRAN, but now you really need R 3.0 so the repo should always be installed. I'll fix that later. Cheers, TIM On Sun, 2013-11-03 at 22:45 +0000, Tony Travis wrote: > Hi, Tim. > > I encountered two problems today when upgrading a recent install of > Ubuntu 12.04.3 LTS to Bio-Linux 7 on my server "kitcat". First, the CRAN > repository is not added, but is preserved if it is found. Second, there > is a conflict between bio-linux-glimmer3 and tigr-glimmer. > > Here is a quick summary of how I installed Bio-Linux 7: > > HTH, > > Tony. > > > Upgrade "kitcat" to Bio-Linux 7 > > # login on "kitcat" and sudo -i > > root at kitcat:~# mkdir upgrade > > cd upgrade > > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh > > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > > ... > > root at kitcat:~/upgrade# tail -20 bl_do_update_to7.log > > Building dependency tree... > > Reading state information... > > Some packages could not be installed. This may mean that you have > > requested an impossible situation or if you are using the unstable > > distribution that some required packages have not yet been created > > or been moved out of Incoming. > > The following information may help to resolve the situation: > > > > The following packages have unmet dependencies. > > galaxy-server-all : Depends: r-cran-prettyr but it is not going to be installed > > Depends: r-cran-leaps but it is not going to be installed > > Depends: r-cran-tcltk2 but it is not going to be installed > > Depends: r-cran-rwave but it is not going to be installed > > Depends: r-cran-wavethresh but it is not going to be installed > > Depends: r-cran-waveslim but it is not going to be installed > > Depends: r-cran-bitops but it is not going to be installed > > Recommends: ucsc-tools-non-free but it is not installable > > Recommends: laj but it is not installable > > E: Unable to correct problems, you have held broken packages. > > Not all packages installed properly - exiting. > > > > # add CRAN mirror - preserved, but not added by bl_do_update_to7.sh > > vim /etc/apt/sources.list.d/nebc-bio-linux-precise.list > > ... > > deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ > > ... > > > > # re-run > > bl_do_update_to7.sh > > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > > ... > > Reading package lists... > > Building dependency tree... > > Reading state information... > > 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. > > > > Verifying that everything installed... > > bio-linux-glimmer3 failed to install > > Not all packages installed properly - exiting. > > > > # check package dependencies > > apt-cache depends bio-linux-glimmer3 > > root at kitcat:~/upgrade# apt-cache depends bio-linux-glimmer3 > > bio-linux-glimmer3 > > Depends: glimmer3 > > Conflicts: > > Conflicts: > > Replaces: > > Replaces: > > Replaces: tigr-glimmer > > glimmer3 > > Replaces: tigr-glimmer:i386 > > glimmer3:i386 > > > > # download > > bl_master_package_list.sh > > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh > > > > # remove tigr-glimmer > > vim bl_master_package_list.sh > > > > ... > > /tigr-glimmer > > dd > > :wq > > > > # edit update script to run bl_master_package_list.sh locally > > > > vim bl_do_update_to7.sh > > > > ... > > root at kitcat:~/upgrade# diff -Naur bl_do_update_to7.sh bl_do_update_to7.sh.orig > > --- bl_do_update_to7.sh 2013-11-03 14:08:25.072271905 +0000 > > +++ bl_do_update_to7.sh.orig 2012-12-03 11:54:38.000000000 +0000 > > @@ -165,8 +165,7 @@ > > # Now the main upgrade - fetch the script and run > > # runurl should come from the PPA > > apt-get install runurl > > -#runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" > > -bash bl_master_package_list.sh > > +runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" > > if [ $? != 0 ] ; then > > echo "Not all packages installed properly - exiting." > > exit 1 > > > > # run again with local modified > > bl_master_package_list.sh > > bash bl_do_update_to7.sh |& tee bl_do_update_to7.log > > > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From jprocter at compbio.dundee.ac.uk Wed Nov 20 12:42:51 2013 From: jprocter at compbio.dundee.ac.uk (Jim Procter) Date: Wed, 20 Nov 2013 17:42:51 +0000 Subject: [Bio-linux-dev] Jalview and JABA workshop & hackathon in Oxford Message-ID: <528CF49B.1010907@compbio.dundee.ac.uk> Hi Bio-linux folks! We will be holding a Jalview and JABAWS residential workshop on the 12th and 13th December at the Medical Sciences Teaching Centre in Oxford. The Jalview and JABA workshop is for anyone who wants to learn how to use Jalview (www.jalview.org) to get the most out of their multiple sequence alignment data. Jalview is a free tool that integrates with the JABA Web Services system (www.compbio.dundee.ac.uk/jabaws/) to access a range of multiple sequence alignment, protein disorder and protein and RNA secondary structure prediction services. This two day workshop includes a one day hands-on training course on the creation and analysis of multiple sequence alignments with Jalview, an evening dinner, and a hackathon and analysis clinic day where you can work on your own problems with the Jalview and JABA team. If you're a developer, then this is a great chance to find out how you can deploy JABA on your own system, and learn how to configure and add new services. Registration costs ?35 and includes lunch and refreshments, and dinner at St Catherine's College on the 12th December. Bed and Breakfast accommodation is also available at St Catherine's college for an additional ten pounds per night. Sign up before *4th December* at: http://www.buyat.dundee.ac.uk/browse/extra_info.asp?compid=1&modid=2&deptid=31&catid=58&prodid=338 We look forward to meeting you in December! Jim, Sasha and Geoff.