From tony.travis at minke-informatics.co.uk Sun Apr 1 09:49:56 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 1 Apr 2018 14:49:56 +0100 Subject: [Bio-linux-list] Updating Bio-Linux In-Reply-To: References: Message-ID: <0ee68b5b-ed99-627e-3fa9-682a813a9638@minke-informatics.co.uk> On 01/04/18 11:41, Abdulrahman MI wrote: > Dear?tony > > Thanks for bio-linux? > I have questions? > How to update the tools like SPAdes, etc to most recent release. Hi, Abdulrahman. You have two options: Compile version 3.11.1 from source: > http://cab.spbu.ru/software/spades/ Or, use the Debian-Med PPA to install version 3.8.1: > https://launchpad.net/~debian-med/+archive/ubuntu/ppa This is what I have installed: > ajt at beluga:~$ apt-cache policy spades > spades: > Installed: (none) > Candidate: 3.8.1+dfsg-1~ubuntu14.04~ppa1 > Version table: > 3.8.1+dfsg-1~ubuntu14.04~ppa1 0 > 500 http://ppa.launchpad.net/debian-med/ppa/ubuntu/ trusty/main amd64 Packages It's very easy to add the Debian-Med PPA to Bio-Linux: > sudo add-apt-repository ppa:debian-med/ppa > sudo apt-get update Please post a message here and on the Debian-Med list if you have any problems installing or running Spades under Bio-Linux 8 / Ubuntu 14.04. > and any plan to update the base Ubuntu from 14 to 16? No, because Ubuntu 18.04 is about to be released, and we will base the next version of Bio-Linux on Ubuntu-MATE 18.04 LTS. This version will make use of the Debian-Med team's hard work packaging bioinformatics software, but will also come with "Bioconda" pre-installed. Thanks for your interest in Bio-Linux and please help to spread the word about our Bio-Linux 8.0.8 point release available from: > http://www.bioinformatics.org/project/?group_id=341 You do not need to re-install Bio-Linux 8.0.7 if you already have it on your PC hard disk: Just make sure you have updated your installation: sudo -i apt update apt full-upgrade However, the new Bio-Linux 8.0.8 .iso file has an updated kernel that better supports modern WiFi chipsets in particular, and all the packages are updated. The Bio-Linux 8.0.8 .iso also has "mdadm" pre-installed, which makes installing Bio-Linux to Linux 'md' software RAID easier. 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 minke-informatics.co.uk Mon Apr 2 18:05:42 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 2 Apr 2018 23:05:42 +0100 Subject: [Bio-linux-list] www.stats.bris.ac.uk Down? In-Reply-To: <3F9E65788480CD4282B12895264CC2140109EEF58E@WN24244.or.providence.org> References: <3F9E65788480CD4282B12895264CC2140109EEF58E@WN24244.or.providence.org> Message-ID: <7ee212a0-9d9a-21bb-3374-9e0adc762aea@minke-informatics.co.uk> On 02/04/18 22:36, Dubay, Christopher J wrote: > [...] > I am not able to connect to one of the update sites (which in my > BioLinux installation is www.stats.bris.ac.uk > ). > > ? > > Is it down for everyone (https://downforeveryoneorjustme.com/ says > everyone)? Is there a mirror somewhere? Hi, Christopher. You're right, it's down for everyone... These might help: > https://cran.r-project.org/bin/linux/ubuntu/ > https://cran.r-project.org/mirrors.html Use this to change your "cran-latest-r.list" APT sources file: > deb https:///bin/linux/ubuntu trusty/ Mine looks like this: > cat /etc/apt/sources.list.d/cran-latest-r.list > #Latest R-cran packages > #deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu trusty/ > #deb-src http://www.stats.bris.ac.uk/R//bin/linux/ubuntu trusty/ > deb http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu trusty/ > deb-src http://mirrors.ebi.ac.uk/CRAN/bin/linux/ubuntu trusty/ However, we are also using Michael Rutter's PPA: https://launchpad.net/~marutter Post a message here to let me know how you get on? 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 Mon Apr 9 09:24:27 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 9 Apr 2018 14:24:27 +0100 Subject: [Bio-linux-list] FW: Biolinux / Firefox web browser In-Reply-To: References: <66bb6b8668264384b08f9fbc8e585f47@OXNETEX02.oxnet.nhs.uk> Message-ID: <9b6de0cc-22d7-ae2f-dca3-bc31cceb5a82@minke-informatics.co.uk> On 09/04/18 13:59, Timms-Wilson, Tracey wrote: > ? > > ? > > *From:* Breen Patrick (RTH) OUH [mailto:Patrick.Breen at ouh.nhs.uk] > *Sent:* 09 April 2018 13:34 > *To:* Timms-Wilson, Tracey > *Subject:* Biolinux / Firefox web browser > > ? > > Dear Tracey > > ? > > Following my phone call from a few minutes ago, I would be grateful for > the assistance of your team with my query. > > ? > > I have been using Biolinux 8, which is downloaded on my MAC laptop, over > the weekend and today for a bioinformatics course I am doing. However, I > have been unable to access the internet, via the FireFox web browser on > Biolinux 8, yesterday and today. I am using the wifi service at Oxford > University Hospitals, and wonder if this could be the issue. I have no > trouble accessing the interne, when I switch over to the MAC operating > system. This is stressing me as I cannot email answers for my project to > the course director. Can you help? Hi, Patrick. Tracey forwarded your email to me and I've CC'ed my reply to the Bio-Linux mailing list in case anyone else is having similar problems. When you say "Bio-Linux 8, which is downloaded to my MAC", do you mean you've actually installed it onto the Mac hard disk or just that you are running Bio-Linux from a downloaded .iso file written to a USB stick? If you are running Bio-Linux fromn a USB-stick, did you download the latest version 8.0.8, which has a newer Linux kernel and WiFi drivers? > https://www.bioinformatics.org/groups/?group_id=341 If you've installed Bio-Linux to your Mac hard disk, you will have to check for updated drivers for the WiFi chipset used in your Mac because we are not allowed to distribute the proprietary drivers needed by some WiFi chipsets. These must be downloaded and installed separately. If you're running Bio-Linux on your Mac as a guest OS under VirtualBox, it should be using the 'native' Mac OS drivers on the host OS. A quick solution to your immediate problem would be to plug your Mac into a wired Ethernet connection, which will work without any problems. You would, in any case, need to do that if you install Bio-Linux to the hard disk and want to update the drivers. If you are running Bio-Linux from a USB-stick, you can save your work to the FAT partition of the Bio-Linux USB-stick if it is only a few small files, or write it to a larger USB-stick or USB-disk in another port on your laptop and email it after rebooting into mac OS. Let us know how you get an and ask your course organiser to post a message to the Bio-Linux mailing list or contact me off-list if you need more help. 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 minke-informatics.co.uk Tue Apr 10 04:53:27 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 10 Apr 2018 10:53:27 +0200 Subject: [Bio-linux-list] FW: Biolinux / Firefox web browser In-Reply-To: <1523308627122.81389@ouh.nhs.uk> References: <66bb6b8668264384b08f9fbc8e585f47@OXNETEX02.oxnet.nhs.uk> <9b6de0cc-22d7-ae2f-dca3-bc31cceb5a82@minke-informatics.co.uk> <1523308627122.81389@ouh.nhs.uk> Message-ID: On 09/04/18 23:17, Breen Patrick (RTH) OUH wrote: > Hi Tony > > Thanks for getting in touch. Hi, Patrick. Please post your messages to the Bio-Linux mailing list because someone there might be able to help you or might have similar problems to you. > I am running Bio-Linux on my Mac as a guest OS under VirtualBox. Can > you advise on how to check that it is using the 'native' MAC drivers, > as I don't really understand this? This is not a Bio-Linux issue, it depends on how you set up networking for the VirtualBox guest OS when you created it. I don't have experience of using VirtualBox with Mac OS as the host and Bio-Linux as the guest. However, a quick Google search showed up lots of networking issues for people who are running VirtualBox on a Mac OS host. This might help: > http://www.bogotobogo.com/Linux/Ubuntu_Desktop_on_Mac_OSX_using_VirtualBox_4_3_II.php BTW, did you import the .ova or did you install it from a .iso file? In any case, when you a network connection, please run in a terminal: sudo -i apt update apt full-upgrade As I mentioned before, it will be a lot easier if you connect your Mac to a wired Ethernet connection. > Is Biolinux any easier to use if I run it off a USB-stick? I had > tried that approach when I first started using Biolinux in january? It is quite easy to run Bio-Linux from a USB-stick, but WiFi may not work depending on which WiFi chipset is in your laptop. This is not a Bio-Linux or Ubuntu issue, it is because the WiFi chips use proprietary firmware that Apple and MicroSoft do not want to be freely distributed. > Any other advice would be most welcome. I would try booting Bio-Linux from a USB-stick with you Mac connected to a wired Ethernet connection or using a USB WiFi dongle that is supported by Ubuntu 14.04 LTS. Let me know how you get on, especially if you can get it to work :-) 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 minke-informatics.co.uk Mon Apr 16 07:29:53 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 16 Apr 2018 12:29:53 +0100 Subject: [Bio-linux-list] FW: biolinux In-Reply-To: References: Message-ID: <71c9a275-2394-f884-4fb9-98a791a524f8@minke-informatics.co.uk> On 16/04/2018 09:13, Timms-Wilson, Tracey wrote: > > *From:* Stefan WECKX [mailto:Stefan.Weckx at vub.be] > *Sent:* 13 April 2018 09:21 > *To:* Timms-Wilson, Tracey > *Subject:* biolinux > > Dear colleague, > > As we are planning to setting up a new linux server for > bioinformatics, I was wondering whether you have plans to release a > BioLinux 9 based on Ubuntu 16.04 LTS? > Hi, Stefan. Tracey forwarded your email to me and I've replied to the Bio-Linux list in case anyone else has the sanme question. Yes, we are planning a release of Bio-Linux 9 but it will be based on Ubuntu-MATE 18.04 LTS not 16.04. The new version of Bio-Linux will include many packages from the Debian-Med team and will also have "Bioconda" pre-installed. You can upgrade Ubuntu 14.04 LTS to 16.04 in Bio-Linux 8, but many package dependencies will be broken and I don't recommend doing the upgrade unless you are willing to fix these dependency problems yourself. I've upgraded a few instances of Bio-Linux 8 based on Ubuntu 14.04 LTS to Ubunti 16.04 LTS and the upgrade is a lot smoother now than it was. Please post your experiences here if you decide to upgrade to Ubuntu 16.04. Thanks, ? Tony. --- This email has been checked for viruses by AVG. http://www.avg.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Mon Apr 16 08:55:23 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 16 Apr 2018 13:55:23 +0100 Subject: [Bio-linux-list] FW: biolinux In-Reply-To: References: <71c9a275-2394-f884-4fb9-98a791a524f8@minke-informatics.co.uk> Message-ID: <6b97fd28-b360-417f-90e3-2a8fddfc7f1e@minke-informatics.co.uk> On 16/04/2018 13:13, Stefan WECKX wrote: > > Hi Tony, > > Thanks for the follow-up. Very good news indeed. Any estimate of > release date? > Hi, Stefan. I attended the 2018 Debian-Med Sprint in Barcelona recently, at which we discussed the overlap between the 'old' binary-only NEBC packages and more recent packages of the upstream software in the Debian-Med Ubuntu PPA. I presented my plans for Bio-Linux 9 and the Debian-Med team were very helpful, as they have been for many years helping to improved Bio-Linux. I argued that it would be better to base Bio-Linux 9 on Ubuntu-MATE 18.04 LTS, because Ubuntu 16.04 LTS is already two years old and the MATE desktop is currently used for Bio-Linux terminal servers and remote desktops. Canonical have d ropped Unity and, in any case, MATE has lower hardware requirements, which is particularly important to people runninbg Bio-Linux on older computers or servers with poor graphics hardware. Ubuntu-MATE 18.04 LTS has not yet been released, but I have been trying out the beta-releases and it looks very good. I expect it to take at lease three months to put together a beta-rlease of Bio-Linux 9 and I will post announcements about it here. Bye, ? Tony. > *From:*Tony Travis > *Sent:* 16 April 2018 13:30 > *To:* Bio-Linux mailing list > *Cc:* Stefan WECKX ; Timms-Wilson, Tracey > > *Subject:* Re: FW: biolinux > > On 16/04/2018 09:13, Timms-Wilson, Tracey wrote: > > *From:* Stefan WECKX [mailto:Stefan.Weckx at vub.be] > *Sent:* 13 April 2018 09:21 > *To:* Timms-Wilson, Tracey > *Subject:* biolinux > > Dear colleague, > > As we are planning to setting up a new linux server for > bioinformatics, I was wondering whether you have plans to release > a BioLinux 9 based on Ubuntu 16.04 LTS? > > > Hi, Stefan. > > Tracey forwarded your email to me and I've replied to the Bio-Linux > list in case anyone else has the sanme question. > > Yes, we are planning a release of Bio-Linux 9 but it will be based on > Ubuntu-MATE 18.04 LTS not 16.04. > > The new version of Bio-Linux will include many packages from the > Debian-Med team and will also have "Bioconda" pre-installed. > > You can upgrade Ubuntu 14.04 LTS to 16.04 in Bio-Linux 8, but many > package dependencies will be broken and I don't recommend doing the > upgrade unless you are willing to fix these dependency problems > yourself. I've upgraded a few instances of Bio-Linux 8 based on Ubuntu > 14.04 LTS to Ubunti 16.04 LTS and the upgrade is a lot smoother now > than it was. Please post your experiences here if you decide to > upgrade to Ubuntu 16.04. > > Thanks, > > ? Tony. > > ------------------------------------------------------------------------ > > Image removed by sender. AVG logo > > > > This email has been checked for viruses by AVG antivirus software. > www.avg.com > > > --- This email has been checked for viruses by AVG. http://www.avg.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ~WRD000.jpg Type: image/jpeg Size: 823 bytes Desc: not available URL: From mkmodi at aau.ac.in Mon Apr 16 09:01:51 2018 From: mkmodi at aau.ac.in (Mahendra Modi) Date: Mon, 16 Apr 2018 18:31:51 +0530 Subject: [Bio-linux-list] FW: biolinux In-Reply-To: <6b97fd28-b360-417f-90e3-2a8fddfc7f1e@minke-informatics.co.uk> References: <71c9a275-2394-f884-4fb9-98a791a524f8@minke-informatics.co.uk> <6b97fd28-b360-417f-90e3-2a8fddfc7f1e@minke-informatics.co.uk> Message-ID: Dear Tony, That is very good news indeed. Expect to get io-Linux 9 by July 2018 or so. Mahendra ________________________ *Prof. Mahendra K Modi* *Head, Agril Biotechnology & Coordinator, DIC* *Assam Agricultural University* *Jorhat 785013, India* On Mon, Apr 16, 2018 at 6:25 PM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 16/04/2018 13:13, Stefan WECKX wrote: > > Hi Tony, > > > > Thanks for the follow-up. Very good news indeed. Any estimate of release > date? > > > Hi, Stefan. > > I attended the 2018 Debian-Med Sprint in Barcelona recently, at which we > discussed the overlap between the 'old' binary-only NEBC packages and more > recent packages of the upstream software in the Debian-Med Ubuntu PPA. I > presented my plans for Bio-Linux 9 and the Debian-Med team were very > helpful, as they have been for many years helping to improved Bio-Linux. > > I argued that it would be better to base Bio-Linux 9 on Ubuntu-MATE 18.04 > LTS, because Ubuntu 16.04 LTS is already two years old and the MATE desktop > is currently used for Bio-Linux terminal servers and remote desktops. > Canonical have d ropped Unity and, in any case, MATE has lower hardware > requirements, which is particularly important to people runninbg Bio-Linux > on older computers or servers with poor graphics hardware. > > Ubuntu-MATE 18.04 LTS has not yet been released, but I have been trying > out the beta-releases and it looks very good. I expect it to take at lease > three months to put together a beta-rlease of Bio-Linux 9 and I will post > announcements about it here. > > Bye, > > Tony. > > > > *From:* Tony Travis > > *Sent:* 16 April 2018 13:30 > *To:* Bio-Linux mailing list > > *Cc:* Stefan WECKX ; > Timms-Wilson, Tracey > *Subject:* Re: FW: biolinux > > > > On 16/04/2018 09:13, Timms-Wilson, Tracey wrote: > > > > > > *From:* Stefan WECKX [mailto:Stefan.Weckx at vub.be ] > *Sent:* 13 April 2018 09:21 > *To:* Timms-Wilson, Tracey > *Subject:* biolinux > > > > Dear colleague, > > > > As we are planning to setting up a new linux server for bioinformatics, I > was wondering whether you have plans to release a BioLinux 9 based on > Ubuntu 16.04 LTS? > > > > > Hi, Stefan. > > Tracey forwarded your email to me and I've replied to the Bio-Linux list > in case anyone else has the sanme question. > > Yes, we are planning a release of Bio-Linux 9 but it will be based on > Ubuntu-MATE 18.04 LTS not 16.04. > > The new version of Bio-Linux will include many packages from the > Debian-Med team and will also have "Bioconda" pre-installed. > > You can upgrade Ubuntu 14.04 LTS to 16.04 in Bio-Linux 8, but many package > dependencies will be broken and I don't recommend doing the upgrade unless > you are willing to fix these dependency problems yourself. I've upgraded a > few instances of Bio-Linux 8 based on Ubuntu 14.04 LTS to Ubunti 16.04 LTS > and the upgrade is a lot smoother now than it was. Please post your > experiences here if you decide to upgrade to Ubuntu 16.04. > > Thanks, > > Tony. > > > ------------------------------ > > [image: Image removed by sender. AVG logo] > > > This email has been checked for viruses by AVG antivirus software. > www.avg.com > > > > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: ~WRD000.jpg Type: image/jpeg Size: 823 bytes Desc: not available URL: From tony.travis at minke-informatics.co.uk Tue Apr 24 10:49:58 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 24 Apr 2018 15:49:58 +0100 Subject: [Bio-linux-list] query biolinux problem In-Reply-To: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> References: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> Message-ID: On 24/04/18 14:48, Pablo Farace wrote: > Good morning Tony, > I installed the Biolinux 8 on my computer, when I run the commands sudo > apt update && sudo apt install I get this: > > > sudo apt update?????????????????????? [10:42] > [...] > signatures couldn't be verified because the public key is not available: > NO_PUBKEY 1397BC53640DB551 > W: There is no public key available for the following key IDs: > 1397BC53640DB551 > W: GPG error: http://www.stats.bris.ac.uk trusty/ Release: The following > signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 > KEYEXPIRED 1445181253 > W: Failed to fetch > http://dl.google.com/linux/chrome/deb/dists/stable/main/binary-i386/Packages? > 404? Not Found [IP: 172.217.162.14 80] > > E: Some index files failed to download. They have been ignored, or old > ones used instead. > > How can I solve the error that appears? I have also seen that sound does > not work, can it be fixed? Hi, Pablo. I've copied my reply to the Bio-linux mailing list in case anyone else has encountered the same problem. Which version of Bio-Linux did you download? It looks like you downloaded Bio-Linux 8.0.7. Please download the latest Bio-Linux 8.0.8 from: > https://www.bioinformatics.org/downloads/index.php?file_id=627 The version of Bio-Linux 8.0.7 available on the NERC website is now out of date and should no longer be used. However, if you want to fix the problems in an installed version of Bio-Linux 8.0.7, you need to edit the APT sources and add a couple of GPG keys: > echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" > /etc/apt/sources.list.d/google-chrome.list> apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 640DB551 > apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 > apt update > apt full-upgrade > apt-cache autoremove Please post a message to the Bio-linux mailing list to let us know how you get on? Thanks, 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 Tue Apr 24 10:55:35 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 24 Apr 2018 15:55:35 +0100 Subject: [Bio-linux-list] query biolinux problem [correction] In-Reply-To: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> References: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> Message-ID: On 24/04/18 14:48, Pablo Farace wrote: > Good morning Tony, > I installed the Biolinux 8 on my computer, when I run the commands sudo > apt update && sudo apt install I get this: > > > sudo apt update?????????????????????? [10:42] > [...] > signatures couldn't be verified because the public key is not available: > NO_PUBKEY 1397BC53640DB551 > W: There is no public key available for the following key IDs: > 1397BC53640DB551 > W: GPG error: http://www.stats.bris.ac.uk trusty/ Release: The following > signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 > KEYEXPIRED 1445181253 > W: Failed to fetch > http://dl.google.com/linux/chrome/deb/dists/stable/main/binary-i386/Packages? > 404? Not Found [IP: 172.217.162.14 80] > > E: Some index files failed to download. They have been ignored, or old > ones used instead. > > How can I solve the error that appears? I have also seen that sound does > not work, can it be fixed? Hi, Pablo. I've copied my reply to the Bio-linux mailing list in case anyone else has encountered the same problem. Which version of Bio-Linux did you download? It looks like you downloaded Bio-Linux 8.0.7. Please download the latest Bio-Linux 8.0.8 from: > https://www.bioinformatics.org/downloads/index.php?file_id=627 The version of Bio-Linux 8.0.7 available on the NERC website is now out of date and should no longer be used. However, if you want to fix the problems in an installed version of Bio-Linux 8.0.7, you need to edit the APT sources and add a couple of GPG keys: > sudo -i > echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" > /etc/apt/sources.list.d/google-chrome.list > apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 640DB551 > apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 > apt update > apt full-upgrade > apt-cache autoremove Please post a message to the Bio-linux mailing list to let us know how you get on? Thanks, 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 Tue Apr 24 11:00:06 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 24 Apr 2018 16:00:06 +0100 Subject: [Bio-linux-list] query biolinux problem [correction#2] In-Reply-To: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> References: <46ea3f983a2e4fbba3d1db3d28c3c907@inta.gob.ar> Message-ID: On 24/04/18 14:48, Pablo Farace wrote: > Good morning Tony, > I installed the Biolinux 8 on my computer, when I run the commands sudo > apt update && sudo apt install I get this: > > > sudo apt update?????????????????????? [10:42] > [...] > signatures couldn't be verified because the public key is not available: > NO_PUBKEY 1397BC53640DB551 > W: There is no public key available for the following key IDs: > 1397BC53640DB551 > W: GPG error: http://www.stats.bris.ac.uk trusty/ Release: The following > signatures were invalid: KEYEXPIRED 1445181253 KEYEXPIRED 1445181253 > KEYEXPIRED 1445181253 > W: Failed to fetch > http://dl.google.com/linux/chrome/deb/dists/stable/main/binary-i386/Packages? > 404? Not Found [IP: 172.217.162.14 80] > > E: Some index files failed to download. They have been ignored, or old > ones used instead. > > How can I solve the error that appears? I have also seen that sound does > not work, can it be fixed? Hi, Pablo. I've copied my reply to the Bio-linux mailing list in case anyone else has encountered the same problem. Which version of Bio-Linux did you download? It looks like you downloaded Bio-Linux 8.0.7. Please download the latest Bio-Linux 8.0.8 from: > https://www.bioinformatics.org/downloads/index.php?file_id=627 The version of Bio-Linux 8.0.7 available on the NERC website is now out of date and should no longer be used. However, if you want to fix the problems in an installed version of Bio-Linux 8.0.7, you need to edit the APT sources and add a couple of GPG keys: > sudo -i > echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" > /etc/apt/sources.list.d/google-chrome.list > apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 640DB551 > apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 > apt update > apt full-upgrade > apt-get autoremove Please post a message to the Bio-linux mailing list to let us know how you get on? Thanks, 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 Mon Apr 30 04:45:27 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 30 Apr 2018 09:45:27 +0100 Subject: [Bio-linux-list] FW: BioLinux Instillation Help In-Reply-To: References: Message-ID: On 30/04/18 08:17, Timms-Wilson, Tracey wrote: > ? > > ? > > *From:*Jennifer Ronholm, Dr. [mailto:jennifer.ronholm at mcgill.ca] > *Sent:* 24 April 2018 19:01 > *To:* Timms-Wilson, Tracey > *Subject:* BioLinux Instillation Help > > ? > > Good Afternoon,? > > ? > > I am attempting to install BioLinux.? > > ? > > However, when I start the instillation, it says that I am not connected > to the internet (even though I am though an ethernet cable). > > ? > > So I continue on with the instillation and then at a certain point, I > get an error that says "The 'grub-efi-amd64-signed' package filed to > install into /target/. Without the GRUB boot loader, the installed > system will not boot." > > ? > > What should I do? Hi, Jen. Tracey forwarded your message to me and I'm CC'ing my reply to the Bio-Linux mailing list in case anyone else has experienced similar problems. Which version of Bio-Linux did you download? Please make sure you are using Bio-Linux 8.0.8 from: > https://www.bioinformatics.org/groups/?group_id=341 This version has an up-to-date kernel, which is more likely to support the Ethernet hardware you have in your computer. Please also run the self-check test on the USB stack or DVD you created in case there are errors or corruption of the medium, which might explain your problems. Let us know how you get on by posting a message to the Bio-Linux list. 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