From alavore at gmail.com Mon Feb 1 07:12:08 2016 From: alavore at gmail.com (Andres Lavore) Date: Mon, 1 Feb 2016 09:12:08 -0300 Subject: [Bio-linux-list] Insatlling Bio-linux 8 Message-ID: Hi, I'm try to installing Bio-linux 8 in a 100GB partition disk in my Laptop. First at all, I have tried to overwrite bio-linux from Ubuntu 14 with the command *wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh, and appeared the following error: * W: Failed to fetch http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/vivid/main/binary-amd64/Packages 404 Not Found W: Failed to fetch http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/vivid/main/binary-i386/Packages 404 Not Found E: Some index files failed to download. They have been ignored, or old ones used instead. I believe thar these 2 packages are wrong and this is the reason that the instalation failed. After that, I tried to install BioLinux booting a USB memory, but when de installation start (after the time time ussage configuration) an error appear telling me that there is an error in the DVD device or in the HDD. Did somebody see these errors before? How is the better way to install Bio-linux8 in a partition disk to mantain my Win10? Thans at all Chear Andres -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Mon Feb 1 07:44:21 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 1 Feb 2016 12:44:21 +0000 Subject: [Bio-linux-list] Insatlling Bio-linux 8 In-Reply-To: References: Message-ID: <56AF5325.1060108@minke-informatics.co.uk> On 01/02/16 12:12, Andres Lavore wrote: > Hi, > > I'm try to installing Bio-linux 8 in a 100GB partition disk in my > Laptop. > > First at all, I have tried to overwrite bio-linux from Ubuntu 14 > with the command /wget -qO- > http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh, and > appeared the following error: / / / > > W: Failed to fetch > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/vivid/main/binary-amd64/Packages > 404 Not Found > > W: Failed to fetch > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/dists/vivid/main/binary-i386/Packages > 404 Not Found Hi, Andres. Bio-Linux is based on Ubuntu 14.04 LTS "Trusty", but it looks like you are running Ubuntu 15.04 "Vivid" - You can't use Tim's "upgrade8.sh" script for "Vivid" unless you downgrade it to Ubuntu 14.04 LTS first. Try running: lsb_release -d It should say: Description: Ubuntu 14.04.3 LTS If not, you won't be able to use Tim's script. > E: Some index files failed to download. They have been ignored, or > old ones used instead. > > > I believe thar these 2 packages are wrong and this is the reason > that the instalation failed. > > > After that, I tried to install BioLinux booting a USB memory, but > when de installation start (after the time time ussage configuration) > an error appear telling me that there is an error in the DVD device > or in the HDD. How did you create your Bio-Linux USB-stick? > Did somebody see these errors before? How is the better way to > install Bio-linux8 in a partition disk to mantain my Win10? It can be quite complicated to install Bio-Linux on a UEFI laptop if you want to preserve the Windows 10 boot-loader. The default Bio-Linux installation does not always detect the Windows "EFI" partition, so you have to installed the EFI version of GRUB manually to get it to work. I've just done exactly what you are trying to do on my colleague's Windows 10 UEFI laptop using one of Tim's standard NEBC Bio-Linux USB-sticks. The only problem that we encountered was updating the EFI boot partition to include a Bio-Linux (Ubuntu) entry in the boot menu. 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 flacchy at gmail.com Wed Feb 3 10:27:31 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Wed, 3 Feb 2016 15:27:31 +0000 Subject: [Bio-linux-list] uptdating softwares on biolinux Message-ID: Hello, In our lab we just install biolinux 8. I am new to biolinux and I have notice that some of the versions of software in biolinux 8 are not the latest (i.e. blast and swarm). I will need to update this versions for all the users so I was wondering if anyone has any advice on how to update them without creating conflicts? I have tried to look at swarm documentation here: https://github.com/torognes/swarm but it seems not to have any information on updating and I am not sure if just downloading the new file will do the trick. Same for ncbi blast, does anyone know a way to update the version on biolinux 8 quickly? Thank you so much for your time Kind regards Flavia -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Wed Feb 3 10:33:56 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 3 Feb 2016 15:33:56 +0000 Subject: [Bio-linux-list] uptdating softwares on biolinux In-Reply-To: References: Message-ID: <56B21DE4.9050300@minke-informatics.co.uk> On 03/02/16 15:27, Flavia Flaviani wrote: > Hello, > > In our lab we just install biolinux 8. I am new to biolinux and I have > notice that some of the versions of software in biolinux 8 are not the > latest (i.e. blast and swarm). I will need to update this versions for > all the users so I was wondering if anyone has any advice on how to > update them without creating conflicts? I have tried to look at swarm > documentation here: https://github.com/torognes/swarm but it seems not > to have any information on updating and I am not sure if just > downloading the new file will do the trick. > > Same for ncbi blast, does anyone know a way to update the version on > biolinux 8 quickly? Hi, Flavia. Before you do anything, make sure your Bio-Linux 8 is up-to-date: sudo apt update sudo apt full-upgrade The .iso image used to create the DVD or USB-stick is just a snapshot of the Bio-Linux + Debian-Med + Debian + Ubuntu repositories at the time it was made: If you don't enable upgrades during an install, the first thing you have to do after installation is to update Bio-Linux. 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 flacchy at gmail.com Wed Feb 3 10:50:50 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Wed, 3 Feb 2016 15:50:50 +0000 Subject: [Bio-linux-list] uptdating softwares on biolinux In-Reply-To: <56B21DE4.9050300@minke-informatics.co.uk> References: <56B21DE4.9050300@minke-informatics.co.uk> Message-ID: Hi Tony, thank you so much for the advice. I will give it a try. just a quick final question, will I have to run both sudo command? We access through Remote desktop connection or ssh into Biolinux, do you reckon I will have to have access to the real machine after the update? Cheers Flavia 2016-02-03 15:33 GMT+00:00 Tony Travis : > On 03/02/16 15:27, Flavia Flaviani wrote: > > Hello, > > > > In our lab we just install biolinux 8. I am new to biolinux and I have > > notice that some of the versions of software in biolinux 8 are not the > > latest (i.e. blast and swarm). I will need to update this versions for > > all the users so I was wondering if anyone has any advice on how to > > update them without creating conflicts? I have tried to look at swarm > > documentation here: https://github.com/torognes/swarm but it seems not > > to have any information on updating and I am not sure if just > > downloading the new file will do the trick. > > > > Same for ncbi blast, does anyone know a way to update the version on > > biolinux 8 quickly? > > Hi, Flavia. > > Before you do anything, make sure your Bio-Linux 8 is up-to-date: > > sudo apt update > sudo apt full-upgrade > > The .iso image used to create the DVD or USB-stick is just a snapshot of > the Bio-Linux + Debian-Med + Debian + Ubuntu repositories at the time it > was made: If you don't enable upgrades during an install, the first > thing you have to do after installation is to update Bio-Linux. > > 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/mailman/listinfo/bio-linux-list > -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Wed Feb 3 11:18:10 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 3 Feb 2016 16:18:10 +0000 Subject: [Bio-linux-list] uptdating softwares on biolinux In-Reply-To: References: <56B21DE4.9050300@minke-informatics.co.uk> Message-ID: <56B22842.3010701@minke-informatics.co.uk> On 03/02/16 15:50, Flavia Flaviani wrote: > Hi Tony, > > thank you so much for the advice. I will give it a try. just a quick > final question, will I have to run both sudo command? Hi, Flavia. No, just get a "root" shell instead - e.g. on my laptop "beluga": > ajt at beluga:~$ sudo -i > [sudo] password for ajt: > root at beluga:~# After that, you have root authority and don't need to use "sudo". I normally access Bio-linux on terminal servers via "ssh" or "x2go" and update them without any problems - The only time you need to access the physical console of a Bio-Linux server is if you need to boot single user to run diagnostics, or do a clean install. In fact, you can do a remote install of Bio-Linux if someone boots the remote server from a DVD or USB-stick locally for you and enables "ssh" for the 'live' user. > We access through > Remote desktop connection or ssh into Biolinux, do you reckon I will > have to have access to the real machine after the update? I recently did remote installations of Bio-Linux on some servers at the Mario Negri Institute in Milan, from my office here in Scotland, with help from my friend in Milan who booted their servers from a Bio-Linux USB-stick and enabled "ssh" for the 'live' user so that I could login. I've used this approach many times before to do remote diagnostics and disaster recovery of Bio-Linux running on remote servers around Europe. With an IPMI connection you can access the remote console directly, but it is a serious security vulnerability to expose IPMI on the Internet. Let me know how you get on? 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 flacchy at gmail.com Thu Feb 4 04:34:57 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Thu, 4 Feb 2016 09:34:57 +0000 Subject: [Bio-linux-list] uptdating softwares on biolinux In-Reply-To: <56B22842.3010701@minke-informatics.co.uk> References: <56B21DE4.9050300@minke-informatics.co.uk> <56B22842.3010701@minke-informatics.co.uk> Message-ID: Hi Tony, I have run the sudo apt update sudo apt full-upgrade but it seems that it didn't upgrade the version of swarm to the latest one. I am not sure if I will have to restart the system, in which case, is it possible to do it remotely? Do you or anyone have any other suggestion? I am not sure if by downloading the packedge and installing it on top of the others will create system issues. Has anyone had this problem before Thank you for all the advice Regards flavia 2016-02-03 16:18 GMT+00:00 Tony Travis : > On 03/02/16 15:50, Flavia Flaviani wrote: > > Hi Tony, > > > > thank you so much for the advice. I will give it a try. just a quick > > final question, will I have to run both sudo command? > > Hi, Flavia. > > No, just get a "root" shell instead - e.g. on my laptop "beluga": > > > ajt at beluga:~$ sudo -i > > [sudo] password for ajt: > > root at beluga:~# > > After that, you have root authority and don't need to use "sudo". > > I normally access Bio-linux on terminal servers via "ssh" or "x2go" and > update them without any problems - The only time you need to access the > physical console of a Bio-Linux server is if you need to boot single > user to run diagnostics, or do a clean install. In fact, you can do a > remote install of Bio-Linux if someone boots the remote server from a > DVD or USB-stick locally for you and enables "ssh" for the 'live' user. > > > We access through > > Remote desktop connection or ssh into Biolinux, do you reckon I will > > have to have access to the real machine after the update? > > I recently did remote installations of Bio-Linux on some servers at the > Mario Negri Institute in Milan, from my office here in Scotland, with > help from my friend in Milan who booted their servers from a Bio-Linux > USB-stick and enabled "ssh" for the 'live' user so that I could login. > > I've used this approach many times before to do remote diagnostics and > disaster recovery of Bio-Linux running on remote servers around Europe. > > With an IPMI connection you can access the remote console directly, but > it is a serious security vulnerability to expose IPMI on the Internet. > > Let me know how you get on? > > 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/mailman/listinfo/bio-linux-list > -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From flacchy at gmail.com Tue Feb 23 11:55:19 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Tue, 23 Feb 2016 16:55:19 +0000 Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder Message-ID: Hi everyone, It's been 3 weeks now since I've started trying to install a program without success on Biolinux. Before writing here I have tried to post for help on Biostar but without much luck... you can view it here ( https://www.biostars.org/p/177810/) and here ( https://www.biostars.org/p/178055/ ) so I have decided to try and ask the biolinux users community. The program I need to install is called Vicuna ( http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna) and it requires ncbi-toolkit. To make it run we need to set the path for the ncbi-tool/lib in the configuration file. Unfortunately I cannot locate it . I have locate the package but when I try find / -name 'ncbi-tools-x11' I am still not able to locate the lib for the ncbi tools. (I have tried all various commands and options but with no success). Did anyone had the same issue in the past? Could anyone help? Thank you so much in advance Flavia -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Tue Feb 23 12:41:53 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 23 Feb 2016 17:41:53 +0000 Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder In-Reply-To: References: Message-ID: <56CC99E1.4020307@minke-informatics.co.uk> On 23/02/16 16:55, Flavia Flaviani wrote: > [...] > locate it . I have locate the package but when I try > > find / -name 'ncbi-tools-x11' > > I am still not able to locate the lib for the ncbi tools. (I have tried > all various commands and options but with no success). > > Did anyone had the same issue in the past? > Could anyone help? Hi, Flavia. First, check that you have the package installed: > dpkg -l ncbi-tools-x11 > Desired=Unknown/Install/Remove/Purge/Hold > | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) > ||/ Name Version Architecture Description > +++-===========================-==================-==================-=========================================================== > ii ncbi-tools-x11 6.1.20120620-7 amd64 NCBI libraries for biology applications (X-based utilities) Then, check where the files are installed: > dpkg -L ncbi-tools-x11 > /. > /usr > /usr/lib > /usr/lib/mime > /usr/lib/mime/packages > /usr/lib/mime/packages/ncbi-tools-x11 > [...] Or, you can find all the packages that installed 'ncbi-tools-x11': > dpkg -S ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png You can also search the entire repository using: > sudo -i > apt update > apt install apt-file > apt-file update > apt-file search ncbi-tools-x11 > ajt at beluga:~$ apt-file search ncbi-tools-x11 > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop > app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop > med-bio: /usr/share/blends/med/menu/ncbi-tools-x11 > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11 > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11 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 avarus at fastmail.fm Tue Feb 23 19:25:23 2016 From: avarus at fastmail.fm (Tim Booth) Date: Wed, 24 Feb 2016 00:25:23 +0000 Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder In-Reply-To: References: Message-ID: <1456273523.681889.530002330.7C481840@webmail.messagingengine.com> Hi Flavia, Three weeks of struggle sounds immensely frustrating. ?If I can't get something to work within about ten minutes I get unhappy. It looks like several people have chipped in suggestions but nobody actually tried downloading Vicuna. ?I did. ?It does require NCBI toolkit v7 or later and I can tell you that this is not pre-packaged for Ubuntu or Bio-Linux. ?There is only ncbi-tools6. ?I tried building ncbi_cxx from source and I run into problems like you did. ?It's very big and complex. ?I suspect this may explain the lack of an Ubuntu package. But before I look more deeply into those issues, I notice that the Vicuna download provides a file: executable/vicuna-omp.static.linux64 And in the same folder is a readme.txt that states the file is ready to run on Linux 64-bit. So what happens if you try just using this? Ie. - in the Vicuna PDF manual jump straight to section 3.2 4 (c) and then in part (d) where it says to run ./bin/vicuna instead run ./executable/vicuna- omp.static.linux64 Any joy? Cheers, TIM On Tue, Feb 23, 2016, at 04:55 PM, Flavia Flaviani wrote: > Hi everyone, > > It's been 3 weeks now since I've started trying to install a program > without success on Biolinux. Before writing here I have tried to post > for help on Biostar but without much luck... you can view it ?here > (https://www.biostars.org/p/177810/) and here > (https://www.biostars.org/p/178055/[1]) so I have decided to try and > ask the biolinux users community. > > The program I need to install is called Vicuna > (http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna) > and it requires ncbi-toolkit. To make it run we need to set the path > for the ncbi-tool/lib ?in the configuration file. Unfortunately I > cannot locate it . I have locate the package but when I try >>> find / -name 'ncbi-tools-x11' > I am still not able to locate the lib for the ncbi tools. (I have > tried all various commands and options but with no success). > > Did anyone had the same issue in the past? Could anyone help? > > > Thank you so much in advance > > Flavia > > -- > Flavia Flaviani > > *PhD student* Department of Molecular and Cell Biology University of > Cape Town, South Africa In collaboration with The marine Biological > Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za > flafla at mba.ac.uk > > _________________________________________________ > Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list -- Of course I'm a technophobe; I program computers for a living! Links: 1. https://www.biostars.org/p/178055/#178060 -------------- next part -------------- An HTML attachment was scrubbed... URL: From flacchy at gmail.com Wed Feb 24 04:17:55 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Wed, 24 Feb 2016 09:17:55 +0000 Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder In-Reply-To: <1456273523.681889.530002330.7C481840@webmail.messagingengine.com> References: <1456273523.681889.530002330.7C481840@webmail.messagingengine.com> Message-ID: Hi Tim, thank you for trying to install it yourself. I have not seen that file so thank you for looking at a possible different solution. I will give it a try and let you know if it works. Thanks again cheers, flavia 2016-02-24 0:25 GMT+00:00 Tim Booth : > Hi Flavia, > > Three weeks of struggle sounds immensely frustrating. If I can't get > something to work within about ten minutes I get unhappy. > > It looks like several people have chipped in suggestions but nobody > actually tried downloading Vicuna. I did. It does require NCBI toolkit v7 > or later and I can tell you that this is not pre-packaged for Ubuntu or > Bio-Linux. There is only ncbi-tools6. I tried building ncbi_cxx from > source and I run into problems like you did. It's very big and complex. I > suspect this may explain the lack of an Ubuntu package. > > But before I look more deeply into those issues, I notice that the Vicuna > download provides a file: > > executable/vicuna-omp.static.linux64 > > And in the same folder is a readme.txt that states the file is ready to > run on Linux 64-bit. So what happens if you try just using this? > > Ie. - in the Vicuna PDF manual jump straight to section 3.2 4 (c) and then > in part (d) where it says to run ./bin/vicuna instead run > ./executable/vicuna-omp.static.linux64 > > Any joy? > > Cheers, > > TIM > > > On Tue, Feb 23, 2016, at 04:55 PM, Flavia Flaviani wrote: > > Hi everyone, > > It's been 3 weeks now since I've started trying to install a program > without success on Biolinux. Before writing here I have tried to post for > help on Biostar but without much luck... you can view it here ( > https://www.biostars.org/p/177810/) and here ( > https://www.biostars.org/p/178055/ > ) so I have decided to try and > ask the biolinux users community. > > The program I need to install is called Vicuna ( > http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna) > and it requires ncbi-toolkit. To make it run we need to set the path for > the ncbi-tool/lib in the configuration file. Unfortunately I cannot locate > it . I have locate the package but when I try > > find / -name 'ncbi-tools-x11' > > I am still not able to locate the lib for the ncbi tools. (I have tried > all various commands and options but with no success). > > Did anyone had the same issue in the past? > Could anyone help? > > > Thank you so much in advance > > Flavia > > -- > Flavia Flaviani > > *PhD student* > Department of Molecular and Cell Biology > University of Cape Town, South Africa > In collaboration with > The marine Biological Association of the UK (Plymouth, UK) > flvfla001 at myuct.ac.za > flafla at mba.ac.uk > > *_______________________________________________* > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > > > > -- > Of course I'm a technophobe; I program computers for a living! > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > > -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML attachment was scrubbed... URL: From flacchy at gmail.com Wed Feb 24 04:54:09 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Wed, 24 Feb 2016 09:54:09 +0000 Subject: [Bio-linux-list] locating ncbi-tools-x11 lib folder In-Reply-To: <56CC99E1.4020307@minke-informatics.co.uk> References: <56CC99E1.4020307@minke-informatics.co.uk> Message-ID: Hi Tony, thanks for helping, again. I've checked and the package is installed: % dpkg -l ncbi-tools-x11 Desired=Unknown/Install/Remove/Purge/Hold | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) ||/ Name Version Architecture Description +++-=========================-=================-=================-======================================================== ii ncbi-tools-x11 6.1.20120620-7 amd64 NCBI libraries for biology applications (X-based util Then I've run the step after sudo -i that you suggested and got this: root at biolinux:~# apt-file search ncbi-tools-x11 app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop app-install-data: /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop med-bio: /usr/share/blends/med/menu/ncbi-tools-x11 ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11 ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11 ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11 Now, I can find the bin folder with your commands, probably I am missing something very stupid here, but I can't seem to locate the /lib for the tools, which is what I need to set in the Vicuna config file before running make. And before testing Tim suggestion to run the /executable/vicuna-omp.static.linux64 I need to run the make file, after have set the /lib, if this make sense. It seems that since the package is there, I should been able to locate the "/lib" for it... I have also went inside each folder linked above but only finding the executable or the bin. Do you have any other suggestion? I am very thankful for all the advice and time you're spending I still have lots to learn so some things that might be obvious are not for me. Thank you so much again regards Flavia 2016-02-23 17:41 GMT+00:00 Tony Travis : > On 23/02/16 16:55, Flavia Flaviani wrote: > > [...] > > locate it . I have locate the package but when I try > > > > find / -name 'ncbi-tools-x11' > > > > I am still not able to locate the lib for the ncbi tools. (I have tried > > all various commands and options but with no success). > > > > Did anyone had the same issue in the past? > > Could anyone help? > > Hi, Flavia. > > First, check that you have the package installed: > > > dpkg -l ncbi-tools-x11 > > Desired=Unknown/Install/Remove/Purge/Hold > > | > Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend > > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) > > ||/ Name Version Architecture > Description > > > +++-===========================-==================-==================-=========================================================== > > ii ncbi-tools-x11 6.1.20120620-7 amd64 > NCBI libraries for biology applications (X-based utilities) > > Then, check where the files are installed: > > > dpkg -L ncbi-tools-x11 > > /. > > /usr > > /usr/lib > > /usr/lib/mime > > /usr/lib/mime/packages > > /usr/lib/mime/packages/ncbi-tools-x11 > > [...] > > Or, you can find all the packages that installed 'ncbi-tools-x11': > > > dpkg -S ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png > > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz > > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif > > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png > > You can also search the entire repository using: > > > sudo -i > > apt update > > apt install apt-file > > apt-file update > > apt-file search ncbi-tools-x11 > > ajt at beluga:~$ apt-file search ncbi-tools-x11 > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:Cn3D-3.0.desktop > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:Psequin.desktop > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:ddv.desktop > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:entrez2.desktop > > app-install-data: > /usr/share/app-install/desktop/ncbi-tools-x11:udv.desktop > > med-bio: /usr/share/blends/med/menu/ncbi-tools-x11 > > ncbi-tools-x11: /usr/lib/mime/packages/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.gz > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/README.sequin.gz > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/changelog.Debian.gz > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/copyright > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firedialog.gif > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/firewall.html > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/affil.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/annot.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/authors.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/cds_edit.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/contact.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/desktop.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/format.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/genbank.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/graphic.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/loc_page.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/logo.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/ncbi_sequin.css > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/net_cfg.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucaln.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucset.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing1.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/nucsing2.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/organism.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/props_pg.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein1.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/protein2.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/sequence.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/submit.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/update.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/validate.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/images/welcome.png > > ncbi-tools-x11: /usr/share/doc/ncbi-tools-x11/sequin.htm > > ncbi-tools-x11: /usr/share/lintian/overrides/ncbi-tools-x11 > > ncbi-tools-x11: /usr/share/menu/ncbi-tools-x11 > > 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 > -- Flavia Flaviani *PhD student* Department of Molecular and Cell Biology University of Cape Town, South Africa In collaboration with The marine Biological Association of the UK (Plymouth, UK) flvfla001 at myuct.ac.za flafla at mba.ac.uk -------------- next part -------------- An HTML 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URL: From jmategkox2 at gmail.com Sun Feb 28 18:16:24 2016 From: jmategkox2 at gmail.com (James Mategko) Date: Sun, 28 Feb 2016 15:16:24 -0800 Subject: [Bio-linux-list] Update Issues with some packages Message-ID: Hello, I just installed Bio-Linux 8 on a new notebook computer and sudo apt-get update is crashing with the following error message: "Reading package lists... Done W: GPG error: http://www.stats.bris.ac.uk trusty/ Release: The following signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 KEYEXPIRED 1445181253" I set up a VM using the most recent .iso file and it has the same issue. I've not encountered this error on vanilla Ubuntu installs. Is the error coming from one of the biolinux packages? Thanks, - James -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Sun Feb 28 19:28:36 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 29 Feb 2016 00:28:36 +0000 Subject: [Bio-linux-list] Update Issues with some packages In-Reply-To: References: Message-ID: <56D390B4.5060203@minke-informatics.co.uk> On 28/02/16 23:16, James Mategko wrote: > Hello, > > I just installed Bio-Linux 8 on a new notebook computer and sudo apt-get > update is crashing with the following error message: > > "Reading package lists... Done > W: GPG error: http://www.stats.bris.ac.uk trusty/ Release: The following > signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 > KEYEXPIRED 1445181253" > > I set up a VM using the most recent .iso file and it has the same issue. > I've not encountered this error on vanilla Ubuntu installs. Is the error > coming from one of the biolinux packages? Hi, James. The problem is the original APT configuration used in the .iso, which is getting quite out-of-date now: You can fix the problem manually: https://www.stats.bris.ac.uk/R/bin/linux/ubuntu/ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 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