From g.cremers at science.ru.nl Fri May 27 09:54:17 2016 From: g.cremers at science.ru.nl (Geert) Date: Fri, 27 May 2016 15:54:17 +0200 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages Message-ID: <1464357257.4448.13.camel@microbpc77> Dear all, I was trying to update Ubuntu 14.04 to Biolinux 8, but I keep running into the same problem. Every time I run the command: wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh it ends with the error message: W: Failed to fetch http://dl.google.com/linux/chrome/deb/dists/stable/Release Unable to find expected entry 'main/binary-i386/Packages' in Release file (Wrong sources.list entry or malformed file) Using the solution from https://bugs.launchpad.net/bio-linux/+bug/1567873, I could get apt-get update to work without error messages, but when I subsequently rerun the command: wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh the error message returns is if nothing happened. Afterwards apt-get update wont work either anymore(same error message). I get the feeling the upgrade8.sh script keeps replacing the files that I need to change in order to get the thing going. I've been running in circles all day so far. Any ideas are therefor more than welcome. Kind regards Geert PS.(now that I am writing an email anyways) I have already a good deal of programs on my computer that will be installed with Biolinux. Will that cause any difficulties. From vyacheslav.a.petrov at mail.ru Fri May 27 10:21:06 2016 From: vyacheslav.a.petrov at mail.ru (=?UTF-8?B?0JLRj9GH0LXRgdC70LDQsiDQn9C10YLRgNC+0LI=?=) Date: Fri, 27 May 2016 17:21:06 +0300 Subject: [Bio-linux-list] =?utf-8?q?Installing_biolinux_8_Google=3Amain/bi?= =?utf-8?q?nary-i386/Packages?= In-Reply-To: <1464357257.4448.13.camel@microbpc77> References: <1464357257.4448.13.camel@microbpc77> Message-ID: <1464358866.211834592@f388.i.mail.ru> Hello! I faced this problem some weeks ago. I think there is some bug in the script emersed after Goggle decided to stop support 32-bit repositories. I can't fix the problem and used Biolinux?disc image for installation. You can find it here? http://environmentalomics.org/bio-linux-download/ ?or here? http://ftp.yzu.edu.tw/Linux/bio-linux-iso/ ?.? With kind regards, Vyacheslav >???????, 27 ??? 2016, 19:54 +06:00 ?? Geert : > >Dear all, > >I was trying to update Ubuntu 14.04 to Biolinux 8, but I keep running >into the same problem. > >Every time I run the command: > >wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo >sh > >it ends with the error message: > >W: Failed to fetch >http://dl.google.com/linux/chrome/deb/dists/stable/Release Unable to >find expected entry 'main/binary-i386/Packages' in Release file (Wrong >sources.list entry or malformed file) > >Using the solution from >https://bugs.launchpad.net/bio-linux/+bug/1567873 , I could get >apt-get update to work without error messages, but when I subsequently >rerun the command: > >wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo >sh > >the error message returns is if nothing happened. > >Afterwards apt-get update wont work either anymore(same error message). > >I get the feeling the upgrade8.sh script keeps replacing the files that >I need to change in order to get the thing going. > >I've been running in circles all day so far. Any ideas are therefor more >than welcome. > > >Kind regards > >Geert > > >PS.(now that I am writing an email anyways) I have already a good deal >of programs on my computer that will be installed with Biolinux. Will >that cause any difficulties. > >_______________________________________________ >Bio-Linux-list mailing list >Bio-Linux-list at bioinformatics.org >http://www.bioinformatics.org/mm/listinfo/bio-linux-list ? ?????????, ?.?.?. ???? ???? ??? ?????? (?.?????) ???????? ?????? vyacheslav.a.petrov at mail.ru -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Fri May 27 11:10:57 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 27 May 2016 16:10:57 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: <1464357257.4448.13.camel@microbpc77> References: <1464357257.4448.13.camel@microbpc77> Message-ID: <57486381.7050505@minke-informatics.co.uk> On 27/05/16 14:54, Geert wrote: > [...] > wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo > sh > > the error message returns is if nothing happened. > > Afterwards apt-get update wont work either anymore(same error message). > > I get the feeling the upgrade8.sh script keeps replacing the files that > I need to change in order to get the thing going. Hi, Geert. You're right that is what is happening, but I thought Tim had fixed the script. Here's a work-around to fix the problem while I check what Tim did: > Work-around for bug in Google Chrome repo > > # create a work folder > ajt at beluga:~$ > mkdir -p src/bioinformatics/Bio-Linux/xtr > > # create a utility script to capture the upgrade scripts > cat > get-upgrade8.sh < #!/bin/bash > #@(#)get-upgrade8.sh 2014-06-30 A.J.Travis > > # > # Wrapper script for downloading Bio-Linux 8 upgrade > # > > export UNPACK_ONLY=1 > > wget http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > chmod +x upgrade8.sh > ./upgrade8.sh > > EOF > > # capture the upgrade scripts > chmod +x get-upgrade8.sh > ./get-upgrade8.sh |& tee ./get-upgrade8.log > --2016-05-27 15:53:34-- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > Resolving nebc.nerc.ac.uk (nebc.nerc.ac.uk)... 192.171.199.66 > Connecting to nebc.nerc.ac.uk (nebc.nerc.ac.uk)|192.171.199.66|:80... connected. > HTTP request sent, awaiting response... 200 OK > Length: 40029 (39K) [text/x-sh] > Saving to: ?upgrade8.sh? > > 0K .......... .......... .......... ......... 100% 7.87M=0.005s > > 2016-05-27 15:53:34 (7.87 MB/s) - ?upgrade8.sh? saved [40029/40029] > > Working in /tmp/tmp.WL6d9WGD2q... > x - created lock directory _sh09863. > x - extracting bio-linux-keyring.deb gzipped > gunzipping file bio-linux-keyring.deb > x - extracting pick_cran_mirror.py gzipped > gunzipping file pick_cran_mirror.py > x - extracting sources.list.clean gzipped > gunzipping file sources.list.clean > x - extracting bl_install_master_list.sh gzipped > gunzipping file bl_install_master_list.sh > x - extracting upgrade_to_8.sh gzipped > gunzipping file upgrade_to_8.sh > x - extracting pseudo_orphans.txt gzipped > gunzipping file pseudo_orphans.txt > x - extracting bl_master_package_list.txt gzipped > gunzipping file bl_master_package_list.txt > x - extracting message1.txt gzipped > gunzipping file message1.txt > x - removed lock directory _sh09863. > Unpack complete in /tmp/tmp.WL6d9WGD2q. Exiting. > > # change to the temp directory (/tmp/tmp.WL6d9WGD2q in this case) > cd /tmp/tmp.WL6d9WGD2q > > # fix the problem repo > cp -ai upgrade_to_8.sh upgrade_to_8.sh.orig > vim upgrade_to_8.sh > ... > deb [arch=amd64] > http://dl.google.com/linux/chrome/deb/ stable main > ... > > # check the edit > diff -Naur upgrade_to_8.sh.orig upgrade_to_8.sh > --- upgrade_to_8.sh.orig 2016-05-27 16:03:19.449332248 +0100 > +++ upgrade_to_8.sh 2016-05-27 16:05:24.475843337 +0100 > @@ -208,7 +208,7 @@ > cat >/etc/apt/sources.list.d/google-chrome.list <<"." > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > # You may comment out this entry, but any other modifications may be lost. > -deb http://dl.google.com/linux/chrome/deb/ stable main > +deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main > . > cat >/etc/apt/sources.list.d/google-talkplugin.list <<"." > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > > > # start the upgrade manually > ./upgrade_to_8.sh HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Fri May 27 11:45:11 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 27 May 2016 16:45:11 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: <57486381.7050505@minke-informatics.co.uk> References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> Message-ID: <57486B87.20604@minke-informatics.co.uk> On 27/05/16 16:10, Tony Travis wrote: > On 27/05/16 14:54, Geert wrote: >> [...] >> wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo >> sh >> >> the error message returns is if nothing happened. >> >> Afterwards apt-get update wont work either anymore(same error message). >> >> I get the feeling the upgrade8.sh script keeps replacing the files that >> I need to change in order to get the thing going. > > Hi, Geert. > > You're right that is what is happening, but I thought Tim had fixed the > script. Here's a work-around to fix the problem while I check what Tim did: Hi, Geert. Tim's sources are here: > https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8 HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Fri May 27 12:04:31 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 27 May 2016 17:04:31 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: <57486B87.20604@minke-informatics.co.uk> References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> <57486B87.20604@minke-informatics.co.uk> Message-ID: <5748700F.7040203@minke-informatics.co.uk> On 27/05/16 16:45, Tony Travis wrote: > [...] > Tim's sources are here: > >> https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8 Steve Moss has already submitted a pull-request about this bug, but I don't have write access and can't merge the patch. I don't want to fork the project so we will have to wait until Tim has time to do it for us. Meanwhile, I'm working on an "upgrade_to-9.sh" for Ubuntu 16.04 LTS. I've upgraded a couple of Bio-Linux 8 / Ubuntu 14.04 instances to 16.04 just to see what does/doesn't work. Galaxy is badly broken and I've not been able to get "x2go-server" working properly yet, but quite a lot of our existing Bio-Linux 8 is working fine under 16.04 with minor surgery to dependencies (more details to follow on the bio-linux-dev list). let us know how you get on with the "upgrade_to_8.sh"? Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at abdn.ac.uk Fri May 27 12:29:01 2016 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 27 May 2016 17:29:01 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: <1464357257.4448.13.camel@microbpc77> References: <1464357257.4448.13.camel@microbpc77> Message-ID: <574875CD.5010901@abdn.ac.uk> On 27/05/16 14:54, Geert wrote: > [...] > PS.(now that I am writing an email anyways) I have already a good deal > of programs on my computer that will be installed with Biolinux. Will > that cause any difficulties. Hi, Geert. Sorry, I forgot to answer your question: I've got a lot of other software installed on my Bio-Linux laptop and as long as you use the Ubuntu package manager to install things you should not have any problems. However, of you install things manually, you might break some Bio-Linux packages. This is particularly true if you install R packages from CRAN and Bioconductor manually to the same locations used by the package manager. Similarly for perl and Python libraries installed using CPAN and PiP. These are not Bio-Linux-specific problems, the conflicts would happen in the same way on a standard Ubuntu system. Bio-Linux has a historical problem about the use of /usr/local, which package managers SHOULD NOT TOUCH but Bio-Linux does. This is because of the way that some of the original bio-linux binary .deb packages were created from conventional 'tarball' installations from source in /usr/local, where software installed from 'tarballs" SHOULD be placed. I've resolved this problem for my own putposes by creating sub-directories in /usr/local and /opt for software I've installed without the package manager, taking care not to overwrite anything that Bio-Linux has put there. You can check what a .deb package installed: dpkg -L package_name e.g. > dpkg -L bio-linux-themes-v8 > /. > /usr > /usr/share > /usr/share/gdm > /usr/share/gdm/themes > /usr/share/gdm/themes/bio-linux5 > /usr/share/gdm/themes/bio-linux5/screenshot.png > /usr/share/gdm/themes/bio-linux5/GdmGreeterTheme.desktop > /usr/share/gdm/themes/bio-linux5/quit.png > /usr/share/gdm/themes/bio-linux5/dna-1400x1250.jpg > /usr/share/gdm/themes/bio-linux5/options.png > /usr/share/gdm/themes/bio-linux5/language.png > ... HTH, Tony. -- 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From jimmy at nete.com Sat May 28 06:51:16 2016 From: jimmy at nete.com (Jimmy Griffin) Date: Sat, 28 May 2016 10:51:16 +0000 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: <5748700F.7040203@minke-informatics.co.uk> References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> <57486B87.20604@minke-informatics.co.uk>, <5748700F.7040203@minke-informatics.co.uk> Message-ID: Anyway to correct the sha1 error message when adding the biolinux repo to Ubuntu 16.04? -------- Original message -------- From: Tony Travis Date: 05/27/2016 12:05 PM (GMT-05:00) To: bio-linux-list at bioinformatics.org Subject: Re: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages On 27/05/16 16:45, Tony Travis wrote: > [...] > Tim's sources are here: > >> https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8 Steve Moss has already submitted a pull-request about this bug, but I don't have write access and can't merge the patch. I don't want to fork the project so we will have to wait until Tim has time to do it for us. Meanwhile, I'm working on an "upgrade_to-9.sh" for Ubuntu 16.04 LTS. I've upgraded a couple of Bio-Linux 8 / Ubuntu 14.04 instances to 16.04 just to see what does/doesn't work. Galaxy is badly broken and I've not been able to get "x2go-server" working properly yet, but quite a lot of our existing Bio-Linux 8 is working fine under 16.04 with minor surgery to dependencies (more details to follow on the bio-linux-dev list). let us know how you get on with the "upgrade_to_8.sh"? Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mm/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Sat May 28 11:24:50 2016 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 28 May 2016 16:24:50 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages In-Reply-To: References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> <57486B87.20604@minke-informatics.co.uk> <5748700F.7040203@minke-informatics.co.uk> Message-ID: <5749B842.7080703@abdn.ac.uk> On 28/05/16 11:51, Jimmy Griffin wrote: > Anyway to correct the sha1 error message when adding the biolinux repo > to Ubuntu 16.04? Hi, Jimmy. As I'm sure you know SHA1 is seriously flawed and will, eventually, be replaced. For anyone who doesn't know why this is important read this: > http://arstechnica.com/security/2012/10/sha1-crypto-algorithm-could-fall-by-2018/ It's the Bio-Linux 8 PPA causing warnings as well as the Google repos: > W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by key 4CCA1EAF950CEE4AB83976DCA040830F7FAC5991 uses weak digest algorithm (SHA1) > W: http://dl.google.com/linux/chrome/deb/dists/stable/Release.gpg: Signature by key 3B068FB4789ABE4AEFA3BB491397BC53640DB551 uses weak digest algorithm (SHA1) > W: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/trusty/InRelease: Signature by key 4A85297A4F26FEE0AE7AC2F4759A8E0E5BA15160 uses weak digest algorithm (SHA1) We don't have any Bio-Linux packages for "xenial" yet, so we have to use the old repo, which uses the SHA1 warning. Please note: This is a warning, not an error, and is caused by the "trusty" PPA repo config. Bye, Tony. -- 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at abdn.ac.uk Sat May 28 11:28:22 2016 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 28 May 2016 16:28:22 +0100 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages [correction] In-Reply-To: <5749B842.7080703@abdn.ac.uk> References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> <57486B87.20604@minke-informatics.co.uk> <5748700F.7040203@minke-informatics.co.uk> <5749B842.7080703@abdn.ac.uk> Message-ID: <5749B916.3070506@abdn.ac.uk> On 28/05/16 16:24, Tony Travis wrote: > O[...] > the old repo, which uses the SHA1 warning. Please note: This is a Oops, I mean "causes" the SHA1 warning... Sorry, Tony. -- 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From g.cremers at science.ru.nl Mon May 30 08:18:00 2016 From: g.cremers at science.ru.nl (Geert) Date: Mon, 30 May 2016 14:18:00 +0200 Subject: [Bio-linux-list] Installing biolinux 8 Google:main/binary-i386/Packages [correction] In-Reply-To: <5749B916.3070506@abdn.ac.uk> References: <1464357257.4448.13.camel@microbpc77> <57486381.7050505@minke-informatics.co.uk> <57486B87.20604@minke-informatics.co.uk> <5748700F.7040203@minke-informatics.co.uk> <5749B842.7080703@abdn.ac.uk> <5749B916.3070506@abdn.ac.uk> Message-ID: <1464610680.21179.0.camel@microbpc77> Thank you all for your comments. I will give it a go this week and see how far I get. Geert. Sorry if this mails get ends twice, I was a bit confused about the email adres I used to subscribe myself. On Sat, 2016-05-28 at 16:28 +0100, Tony Travis wrote: > On 28/05/16 16:24, Tony Travis wrote: > > O[...] > > the old repo, which uses the SHA1 warning. Please note: This is a > > Oops, I mean "causes" the SHA1 warning... > > Sorry, > > Tony. > > -- > 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. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list From pulnimar at yahoo.com Mon May 30 16:40:29 2016 From: pulnimar at yahoo.com (Robert Evans) Date: Mon, 30 May 2016 20:40:29 +0000 (UTC) Subject: [Bio-linux-list] 'Uninstalling' bio-linux References: <317088391.1374941.1464640829668.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> Hello, I've had Biolinux on my personal computer for a few years but haven't used the bioinformatics programs.? I'd like to 'downgrade' to Ubuntu LTS, and then transition to the regular 6 month updates. Is there a way I can do this without messing the system up?? Preferably also without having to reinstall the OS. Thanks,Robert -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Mon May 30 19:22:29 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 31 May 2016 00:22:29 +0100 Subject: [Bio-linux-list] 'Uninstalling' bio-linux In-Reply-To: <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> References: <317088391.1374941.1464640829668.JavaMail.yahoo.ref@mail.yahoo.com> <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> Message-ID: <574CCB35.4060302@minke-informatics.co.uk> On 30/05/16 21:40, Robert Evans wrote: > Hello, > > I've had Biolinux on my personal computer for a few years but haven't > used the bioinformatics programs. I'd like to 'downgrade' to Ubuntu > LTS, and then transition to the regular 6 month updates. > > Is there a way I can do this without messing the system up? Preferably > also without having to reinstall the OS. Hi, Robert. I've got a script that will generate a list of packages to 'dselect': > https://c6c327180cc0273ce5f218d003699c8b3cb652d4.googledrive.com/host/0B-h6GDwW40mtTEctZldjZG4xdTQ/ It compares the filesystem 'manifest' of a live DVD with the packages that are installed on the local system, or the packages installed on two different hosts e.g. Bio-Linux 8 on "wildcat" vs Ubuntu 14.04: Extract the tar file and try it out like this: > rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost ubuntu-14.04-desktop.sel > abyss deinstall > acacia deinstall > account-plugin-windows-live install > aglfn deinstall > agrep deinstall > alacarte deinstall > amap-align deinstall > ampliconnoise deinstall > ant-gcj deinstall > ant deinstall > [...] > xscreensaver-data deinstall > xscreensaver-gl deinstall > xsltproc deinstall > xtrans-dev deinstall > xvnc4viewer deinstall > zim deinstall > zlib1g-dev deinstall > zlib1g:i386 deinstall > zsh-common deinstall > zsh deinstall This is a list of 'dselect-upgrade' package selections that should be "installed" or "deinstalled": I use it to audit my Bio-Linux systems. You can install it, and add any other package selections. You can also use it to compare the package selections installed on two hosts e.g. > rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost alleycat | head > 3dm2 install > account-plugin-identica install > agrep deinstall > alacarte deinstall > ant-gcj deinstall > antlr3 deinstall > ant-optional-gcj deinstall > apparmor-utils deinstall > apport-symptoms deinstall > attr deinstall > [...] > x11proto-xinerama-dev deinstall > xaw3dg:i386 install > xbrlapi deinstall > xfonts-100dpi deinstall > xfonts-75dpi deinstall > xindy deinstall > xindy-rules deinstall > xscreensaver-data deinstall > xserver-xorg-lts-saucy install > zim deinstall The results show how to change the first host to match the manifest selections or the packages that are installed on the second host. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From pulnimar at yahoo.com Mon May 30 20:06:42 2016 From: pulnimar at yahoo.com (Robert Evans) Date: Tue, 31 May 2016 00:06:42 +0000 (UTC) Subject: [Bio-linux-list] 'Uninstalling' bio-linux In-Reply-To: <574CCB35.4060302@minke-informatics.co.uk> References: <317088391.1374941.1464640829668.JavaMail.yahoo.ref@mail.yahoo.com> <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> <574CCB35.4060302@minke-informatics.co.uk> Message-ID: <827633664.1477514.1464653202492.JavaMail.yahoo@mail.yahoo.com> Thanks Tony, I don't necessarily want to uninstall everything that isn't vanilla Ubuntu (I've installed various programs over the years), I just want to get the system set up in such a way that it will upgrade the core OS and utilities along the standard Ubuntu upgrade paths instead of the Biolinux/LTS upgrade paths. I don't know if your tool does that?? I'm quite happy manually uninstalling individual packages after deciding not to use them. I've considered deselecting/deleting the Biolonux repositories in the Software Updater, and switching to upgrade to all new Ubuntu releases (not just LTS or the next Biolinux).? But I don't know if doing so will mangle things vis-a-vis any Biolinux updater scripts which may be in the system. Would doing this solve the primary issue of being on a Biolinux upgrade path versus an Ubuntu upgrade path? I guess I should have made this clearer initially. Thanks,Robert On Monday, May 30, 2016 4:22 PM, Tony Travis wrote: On 30/05/16 21:40, Robert Evans wrote: > Hello, > > I've had Biolinux on my personal computer for a few years but haven't > used the bioinformatics programs.? I'd like to 'downgrade' to Ubuntu > LTS, and then transition to the regular 6 month updates. > > Is there a way I can do this without messing the system up?? Preferably > also without having to reinstall the OS. Hi, Robert. I've got a script that will generate a list of packages to 'dselect': > https://c6c327180cc0273ce5f218d003699c8b3cb652d4.googledrive.com/host/0B-h6GDwW40mtTEctZldjZG4xdTQ/ It compares the filesystem 'manifest' of a live DVD with the packages that are installed on the local system, or the packages installed on two different hosts e.g. Bio-Linux 8 on "wildcat" vs Ubuntu 14.04: Extract the tar file and try it out like this: > rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost ubuntu-14.04-desktop.sel > abyss??? ??? ??? ??? ??? ??? deinstall > acacia??? ??? ??? ??? ??? ??? deinstall > account-plugin-windows-live? ? ? ? ? ? ? ? ? ? install > aglfn??? ??? ??? ??? ??? ??? deinstall > agrep??? ??? ??? ??? ??? ??? deinstall > alacarte??? ??? ??? ??? ??? deinstall > amap-align??? ??? ??? ??? ??? deinstall > ampliconnoise??? ??? ??? ??? ??? deinstall > ant-gcj??? ??? ??? ??? ??? ??? deinstall > ant??? ??? ??? ??? ??? ??? deinstall > [...] > xscreensaver-data??? ??? ??? ??? deinstall > xscreensaver-gl??? ??? ??? ??? ??? deinstall > xsltproc??? ??? ??? ??? ??? deinstall > xtrans-dev??? ??? ??? ??? ??? deinstall > xvnc4viewer??? ??? ??? ??? ??? deinstall > zim??? ??? ??? ??? ??? ??? deinstall > zlib1g-dev??? ??? ??? ??? deinstall > zlib1g:i386??? ??? ??? ??? ??? deinstall > zsh-common??? ??? ??? ??? ??? deinstall > zsh??? ??? ??? ??? ??? ??? deinstall This is a list of 'dselect-upgrade' package selections that should be "installed" or "deinstalled": I use it to audit my Bio-Linux systems. You can install it, and add any other package selections. You can also use it to compare the package selections installed on two hosts e.g. > rwt017 at wildcat:~/Desktop/dpkg-dsel$ ./dpkg-dsel localhost alleycat | head > 3dm2??? ??? ??? ??? ??? ??? install > account-plugin-identica??? ??? ??? ??? install > agrep??? ??? ??? ??? ??? ??? deinstall > alacarte??? ??? ??? ??? ??? deinstall > ant-gcj??? ??? ??? ??? ??? ??? deinstall > antlr3??? ??? ??? ??? ??? ??? deinstall > ant-optional-gcj??? ??? ??? ??? deinstall > apparmor-utils??? ??? ??? ??? ??? deinstall > apport-symptoms??? ??? ??? ??? ??? deinstall > attr??? ??? ??? ??? ??? ??? deinstall > [...] > x11proto-xinerama-dev??? ??? ??? ??? deinstall > xaw3dg:i386??? ??? ??? ??? ??? install > xbrlapi??? ??? ??? ??? ??? ??? deinstall > xfonts-100dpi??? ??? ??? ??? ??? deinstall > xfonts-75dpi??? ??? ??? ??? ??? deinstall > xindy??? ??? ??? ??? ??? ??? deinstall > xindy-rules??? ??? ??? ??? ??? deinstall > xscreensaver-data??? ??? ??? ??? deinstall > xserver-xorg-lts-saucy??? ??? ??? ??? install > zim??? ??? ??? ??? ??? ??? deinstall The results show how to change the first host to match the manifest selections or the packages that are installed on the second host. HTH, ? Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mm/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Mon May 30 20:31:23 2016 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 31 May 2016 01:31:23 +0100 Subject: [Bio-linux-list] 'Uninstalling' bio-linux In-Reply-To: <827633664.1477514.1464653202492.JavaMail.yahoo@mail.yahoo.com> References: <317088391.1374941.1464640829668.JavaMail.yahoo.ref@mail.yahoo.com> <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> <574CCB35.4060302@minke-informatics.co.uk> <827633664.1477514.1464653202492.JavaMail.yahoo@mail.yahoo.com> Message-ID: <574CDB5B.8010509@abdn.ac.uk> On 31/05/16 01:06, Robert Evans wrote: > Thanks Tony, > > I don't necessarily want to uninstall everything that isn't vanilla > Ubuntu (I've installed various programs over the years), I just want to > get the system set up in such a way that it will upgrade the core OS and > utilities along the standard Ubuntu upgrade paths instead of the > Biolinux/LTS upgrade paths. Hi, Robert. My script won't install/deinstall any packages - It just reports what you would have to install/deinstall to reconcile differences between an installed Bio-Linux (or Ubuntu) system and a list of packages based on the 'manifest' file present on a 'live' Ubuntu DVD or another host. > I don't know if your tool does that? I'm quite happy manually > uninstalling individual packages after deciding not to use them. That's what my script is for: It will simply list the packages you have installed that are not part of the 'vanilla' Ubuntu distribution. You decide what to keep and what to uninstall - I wrote it to use with: dpkg --set-selections apt-get dselect-upgrade However, now I use it to generate a list of packages for: apt install ... apt remove ... > I've considered deselecting/deleting the Biolonux repositories in the > Software Updater, and switching to upgrade to all new Ubuntu releases > (not just LTS or the next Biolinux). But I don't know if doing so will > mangle things vis-a-vis any Biolinux updater scripts which may be in the > system. You will probably break a lot of packages if you do: It's advisable to remove all your 'bio-linux*' packages before removing the repositories or you risk dependency 'hell' :-( > Would doing this solve the primary issue of being on a Biolinux upgrade > path versus an Ubuntu upgrade path? Yes, as long as you remove ALL your Bio-Linux packages before removing the Bio-Linux repositories from your configuration. HTH, Tony. -- 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From pulnimar at yahoo.com Mon May 30 20:52:29 2016 From: pulnimar at yahoo.com (Robert Evans) Date: Tue, 31 May 2016 00:52:29 +0000 (UTC) Subject: [Bio-linux-list] 'Uninstalling' bio-linux In-Reply-To: <574CDB5B.8010509@abdn.ac.uk> References: <317088391.1374941.1464640829668.JavaMail.yahoo.ref@mail.yahoo.com> <317088391.1374941.1464640829668.JavaMail.yahoo@mail.yahoo.com> <574CCB35.4060302@minke-informatics.co.uk> <827633664.1477514.1464653202492.JavaMail.yahoo@mail.yahoo.com> <574CDB5B.8010509@abdn.ac.uk> Message-ID: <1545629197.1516386.1464655949446.JavaMail.yahoo@mail.yahoo.com> Thanks a lot Tony! Robert On Monday, May 30, 2016 5:31 PM, Tony Travis wrote: On 31/05/16 01:06, Robert Evans wrote: > Thanks Tony, > > I don't necessarily want to uninstall everything that isn't vanilla > Ubuntu (I've installed various programs over the years), I just want to > get the system set up in such a way that it will upgrade the core OS and > utilities along the standard Ubuntu upgrade paths instead of the > Biolinux/LTS upgrade paths. Hi, Robert. My script won't install/deinstall any packages - It just reports what you would have to install/deinstall to reconcile differences between an installed Bio-Linux (or Ubuntu) system and a list of packages based on the 'manifest' file present on a 'live' Ubuntu DVD or another host. > I don't know if your tool does that?? I'm quite happy manually > uninstalling individual packages after deciding not to use them. That's what my script is for: It will simply list the packages you have installed that are not part of the 'vanilla' Ubuntu distribution. You decide what to keep and what to uninstall - I wrote it to use with: ? dpkg --set-selections ? apt-get dselect-upgrade However, now I use it to generate a list of packages for: ? apt install ... ? apt remove ... > I've considered deselecting/deleting the Biolonux repositories in the > Software Updater, and switching to upgrade to all new Ubuntu releases > (not just LTS or the next Biolinux).? But I don't know if doing so will > mangle things vis-a-vis any Biolinux updater scripts which may be in the > system. You will probably break a lot of packages if you do: It's advisable to remove all your 'bio-linux*' packages before removing the repositories or you risk dependency 'hell' :-( > Would doing this solve the primary issue of being on a Biolinux upgrade > path versus an Ubuntu upgrade path? Yes, as long as you remove ALL your Bio-Linux packages before removing the Bio-Linux repositories from your configuration. HTH, ? Tony. -- 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. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mm/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: