From sararassner at hotmail.com Wed Jun 8 07:31:56 2016 From: sararassner at hotmail.com (Sara Rassner) Date: Wed, 8 Jun 2016 11:31:56 +0000 Subject: [Bio-linux-list] VB guest window resizing problem Message-ID: Hello, I've been running Bio-Linux 8 in VirtualBox for some time and all of a sudden it's throwing up some issues related to VirtualBox. Yesterday, it would not complete booting up, but get stuck on a black screen after the green Bio-Linux 8 logo with the green dots. After some repeated reloading of guest additions I got to the point where it would boot normally, but now I can no longer resize the Bio-Linux desktop within the guest window, but rather I'm stuck with a very small one (640x480, I think). In the past this has been a guest additions related problem, but this time I'm not sure how to solve it. I'm running VirtualBox Version 5.0.20 r106931 with Extension pack 5.0.20 r106931 and the most up-to-date Guest Additions (that came with the 5.0.20 update). After reading suggestions elsewhere, I tried using Guest Additions 5.0.16. This didn't work, but in the process of swapping between the two guest additions versions, I managed to move from Bio-Linux not booting properly to booting. But I still can't resize the window. If it helps: In the guest window, the 'Auto-resize guest display' and 'virtual screen1' resizing options are all greyed out. I should say that I've also got Mageia 5 in VB and that is running absolutely fine, window resizing as it should etc. Any suggestions for how to solve this problem would be greatly appreciated! Thank you, Sara -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Wed Jun 8 09:36:04 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 8 Jun 2016 14:36:04 +0100 Subject: [Bio-linux-list] VB guest window resizing problem In-Reply-To: References: Message-ID: <57581F44.9000905@minke-informatics.co.uk> On 08/06/16 12:31, Sara Rassner wrote: > Hello, > > I've been running Bio-Linux 8 in VirtualBox for some time and all of a > sudden it's throwing up some issues related to VirtualBox. > > Yesterday, it would not complete booting up, but get stuck on a black > screen after the green Bio-Linux 8 logo with the green dots. After some > repeated reloading of guest additions I got to the point where it would > boot normally, but now I can no longer resize the Bio-Linux desktop > within the guest window, but rather I'm stuck with a very small one > (640x480, I think). In the past this has been a guest additions related > problem, but this time I'm not sure how to solve it. Hi, Sara. If you press the 'Esc' key, you will see the boot messages, which might help you to work out what is going wrong. Are you running the 'OVA' VM that Tim created or did you install Bio-Linux from an 'ISO' image? > I'm running VirtualBox Version 5.0.20 r106931 with Extension pack 5.0.20 > r106931 and the most up-to-date Guest Additions (that came with the > 5.0.20 update). After reading suggestions elsewhere, I tried using Guest > Additions 5.0.16. This didn't work, but in the process of swapping > between the two guest additions versions, I managed to move from > Bio-Linux not booting properly to booting. But I still can't resize the > window. If it helps: In the guest window, the 'Auto-resize guest > display' and 'virtual screen1' resizing options are all greyed out. What is your host OS? > I should say that I've also got Mageia 5 in VB and that is running > absolutely fine, window resizing as it should etc. One problem might be running Unity, which requires hardware graphics acceleration. Without it, Bio-Linux/Ubuntu 14.04 will default to a low resolution screen and performance will be terrible :-( > Any suggestions for how to solve this problem would be greatly appreciated! Please give us some more details about the host OS and which Bio-Linux VM you're using. It would also be useful to know if you've upgraded your Bio-Linux 8? 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 avarus at fastmail.fm Wed Jun 8 18:21:33 2016 From: avarus at fastmail.fm (Tim Booth) Date: Wed, 08 Jun 2016 23:21:33 +0100 Subject: [Bio-linux-list] VB guest window resizing problem In-Reply-To: <57581F44.9000905@minke-informatics.co.uk> References: <57581F44.9000905@minke-informatics.co.uk> Message-ID: <1465424493.2263650.632138089.120D825F@webmail.messagingengine.com> Hi Sara, The version of the guest additions that come with VirtualBox are not necessarily compatible with the version of the X server that comes with Ubuntu. I'd highly recommend sticking with the virtualbox-guest-x11 package that comes with Ubuntu. Has that somehow been uninstalled? I've seen various VirtualBox installations messed up by people who thought they could "optimise" their installations by installing different drivers but from what you say it was a regular update that caused the problem. Maybe an update didn't quite stick? Could you please check that: 1) There are no broken or part-installed packages reported by apt. 2) There are no fglrx or nvidia packages installed (dpkg -l | grep 'fglrx\|nvidia' should list nothing) 3) You have not somehow switched to the compatibility X server (dpkg -l | grep 'xserver-xorg' should not show any -lts- packages) You could also post your /var/log/Xorg.0.log file to the list. The answer is quite likely buried somewhere in there, even if it doesn't make much sense to you. Cheers, TIM On Wed, Jun 8, 2016, at 02:36 PM, Tony Travis wrote: > On 08/06/16 12:31, Sara Rassner wrote: > > Hello, > > > > I've been running Bio-Linux 8 in VirtualBox for some time and all of a > > sudden it's throwing up some issues related to VirtualBox. > > > > Yesterday, it would not complete booting up, but get stuck on a black > > screen after the green Bio-Linux 8 logo with the green dots. After some > > repeated reloading of guest additions I got to the point where it would > > boot normally, but now I can no longer resize the Bio-Linux desktop > > within the guest window, but rather I'm stuck with a very small one > > (640x480, I think). In the past this has been a guest additions related > > problem, but this time I'm not sure how to solve it. > > Hi, Sara. > > If you press the 'Esc' key, you will see the boot messages, which might > help you to work out what is going wrong. Are you running the 'OVA' VM > that Tim created or did you install Bio-Linux from an 'ISO' image? > > > I'm running VirtualBox Version 5.0.20 r106931 with Extension pack 5.0.20 > > r106931 and the most up-to-date Guest Additions (that came with the > > 5.0.20 update). After reading suggestions elsewhere, I tried using Guest > > Additions 5.0.16. This didn't work, but in the process of swapping > > between the two guest additions versions, I managed to move from > > Bio-Linux not booting properly to booting. But I still can't resize the > > window. If it helps: In the guest window, the 'Auto-resize guest > > display' and 'virtual screen1' resizing options are all greyed out. > > What is your host OS? > > > I should say that I've also got Mageia 5 in VB and that is running > > absolutely fine, window resizing as it should etc. > > One problem might be running Unity, which requires hardware graphics > acceleration. Without it, Bio-Linux/Ubuntu 14.04 will default to a low > resolution screen and performance will be terrible :-( > > > Any suggestions for how to solve this problem would be greatly appreciated! > > Please give us some more details about the host OS and which Bio-Linux > VM you're using. It would also be useful to know if you've upgraded your > Bio-Linux 8? > > 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 -- Of course I'm a technophobe; I program computers for a living! From flacchy at gmail.com Fri Jun 10 12:07:25 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Fri, 10 Jun 2016 17:07:25 +0100 Subject: [Bio-linux-list] Sickle biolinux 8 Message-ID: Hi everyone, I have been asked to installed sickle on our biolinux machine and before installing something that was already installed I've visited the biolinux page http://environmentalomics.org/bio-linux-software-list/ Here I can see that sicke should be available directly in biolinux: sickle 1.33 windowed adaptive trimming tool for FASTQ files using quality When we type in the terminal sickle we get the message :"No command 'sickle' found, " so I have tried: $ dpkg -s sickle and I got this message: $dpkg-query: package 'sickle' is not installed and no information is available Use dpkg --info (= dpkg-deb --info) to examine archive files, and dpkg --contents (= dpkg-deb --contents) to list their contents. Would you advise me to install the program from github or is there something I am missing for which I cannot access the preinstalled one? thank you for the suggestions 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 Fri Jun 10 13:24:47 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 10 Jun 2016 18:24:47 +0100 Subject: [Bio-linux-list] Sickle biolinux 8 In-Reply-To: References: Message-ID: <575AF7DF.80809@minke-informatics.co.uk> On 10/06/16 17:07, Flavia Flaviani wrote: > Hi everyone, > > I have been asked to installed sickle on our biolinux machine and before > installing something that was already installed I've visited the > biolinux page http://environmentalomics.org/bio-linux-software-list/ > > Here I can see that sicke should be available directly in biolinux: > > > sickle 1.33 windowed adaptive trimming tool for FASTQ files using quality > > > When we type in the terminal sickle we get the message :"No command > 'sickle' found, " > > > > so I have tried: > > $ dpkg -s sickle > > > and I got this message: > > $dpkg-query: package 'sickle' is not installed and no information is > available > Use dpkg --info (= dpkg-deb --info) to examine archive files, > and dpkg --contents (= dpkg-deb --contents) to list their contents. > > > Would you advise me to install the program from github or is there > something I am missing for which I cannot access the preinstalled one? Hi, Flavia. You should only use "dpkg" for low-level tasks when you really have to. For example to fix things that are broken and for installing downloaded .deb packages manually (although "gdebi" is easier to use). You would be better using the high-level "apt" command instead. First update the "apt" database: > root at wildcat:~# apt update > Ign http://extras.ubuntu.com trusty InRelease > Ign http://archive.ubuntu.com precise InRelease > [...] Then search for e.g. the "sickle" package in the repositories: > root at wildcat:~# apt search sickle > Sorting... Done > Full Text Search... Done > r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all > GNU R package "Panel Data Analysis with Heterogeneous Time > > sickle/trusty,now 1.33-1biolinux1 amd64 [installed] > windowed adaptive trimming tool for FASTQ files using quality Having found that there is, indeed, a "sickle" package, you can show details about the package and its dependencies: > root at wildcat:~# apt show sickle > Package: sickle > Priority: optional > Section: science > Installed-Size: 74.8 kB > Maintainer: Debian Med Packaging Team > Version: 1.33-1biolinux1 > Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4) > Download-Size: 17.3 kB > APT-Manual-Installed: yes > APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages > Description: windowed adaptive trimming tool for FASTQ files using quality > Most modern sequencing technologies produce reads that have deteriorating > quality towards the 3'-end. Incorrectly called bases here negatively impact > assembles, mapping, and downstream bioinformatics analyses. > . > Sickle is a tool that uses sliding windows along with quality and length > thresholds to determine when quality is sufficiently low to trim the 3'-end > of reads. It will also discard reads based upon the length threshold. It takes > the quality values and slides a window across them whose length is 0.1 times > the length of the read. If this length is less than 1, then the window is set > to be equal to the length of the read. Otherwise, the window slides along the > quality values until the average quality in the window drops below the > threshold. At that point the algorithm determines where in the window the drop > occurs and cuts both the read and quality strings there. However, if the cut > point is less than the minimum length threshold, then the read is discarded > entirely. > . > Sickle supports four types of quality values: Illumina, Solexa, Phred, and > Sanger. Note that the Solexa quality setting is an approximation (the actual > conversion is a non-linear transformation). The end approximation is close. > . > Sickle also supports gzipped file inputs. You can also see if other versions or upgrade candidates are available: > root at wildcat:~# apt-cache policy sickle > sickle: > Installed: 1.33-1biolinux1 > Candidate: 1.33-1biolinux1 > Version table: > *** 1.33-1biolinux1 0 > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages > 100 /var/lib/dpkg/status 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 Sat Jun 11 06:59:08 2016 From: flacchy at gmail.com (Flavia Flaviani) Date: Sat, 11 Jun 2016 11:59:08 +0100 Subject: [Bio-linux-list] Sickle biolinux 8 In-Reply-To: <575AF7DF.80809@minke-informatics.co.uk> References: <575AF7DF.80809@minke-informatics.co.uk> Message-ID: Hi Tony, thank you for your advice. I have run all your adviced commnads :~$ apt search sickle Sorting... Done Full Text Search... Done r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all GNU R package "Panel Data Analysis with Heterogeneous Time sickle/trusty 1.33-1biolinux1 amd64 windowed adaptive trimming tool for FASTQ files using quality flafla at biolinux:~$ flafla at biolinux:~$ apt show sickle Package: sickle Priority: optional Section: science Installed-Size: 74.8 kB Maintainer: Debian Med Packaging Team < debian-med-packaging at lists.alioth.debian.org> Version: 1.33-1biolinux1 Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4) Download-Size: 17.3 kB APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages Description: windowed adaptive trimming tool for FASTQ files using quality Most modern sequencing technologies produce reads that have deteriorating quality towards the 3'-end. Incorrectly called bases here negatively impact assembles, mapping, and downstream bioinformatics analyses. . Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads. It will also discard reads based upon the length threshold. It takes the quality values and slides a window across them whose length is 0.1 times the length of the read. If this length is less than 1, then the window is set to be equal to the length of the read. Otherwise, the window slides along the quality values until the average quality in the window drops below the threshold. At that point the algorithm determines where in the window the drop occurs and cuts both the read and quality strings there. However, if the cut point is less than the minimum length threshold, then the read is discarded entirely. . Sickle supports four types of quality values: Illumina, Solexa, Phred, and Sanger. Note that the Solexa quality setting is an approximation (the actual conversion is a non-linear transformation). The end approximation is close. . Sickle also supports gzipped file inputs. BUT in the last command I get this : ~$ apt-cache policy sickle sickle: Installed: (none) Candidate: 1.33-1biolinux1 Version table: 1.33-1biolinux1 0 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main amd64 Packages So it seems that it's there but not installed. Can you advise me on how to fix this? thank you so much in advance, Regards Flavia 2016-06-10 18:24 GMT+01:00 Tony Travis : > On 10/06/16 17:07, Flavia Flaviani wrote: > > Hi everyone, > > > > I have been asked to installed sickle on our biolinux machine and before > > installing something that was already installed I've visited the > > biolinux page http://environmentalomics.org/bio-linux-software-list/ > > > > Here I can see that sicke should be available directly in biolinux: > > > > > > sickle 1.33 windowed adaptive trimming tool for FASTQ files > using quality > > > > > > When we type in the terminal sickle we get the message :"No command > > 'sickle' found, " > > > > > > > > so I have tried: > > > > $ dpkg -s sickle > > > > > > and I got this message: > > > > $dpkg-query: package 'sickle' is not installed and no information is > > available > > Use dpkg --info (= dpkg-deb --info) to examine archive files, > > and dpkg --contents (= dpkg-deb --contents) to list their contents. > > > > > > Would you advise me to install the program from github or is there > > something I am missing for which I cannot access the preinstalled one? > > Hi, Flavia. > > You should only use "dpkg" for low-level tasks when you really have to. > For example to fix things that are broken and for installing downloaded > .deb packages manually (although "gdebi" is easier to use). You would be > better using the high-level "apt" command instead. First update the > "apt" database: > > > root at wildcat:~# apt update > > Ign http://extras.ubuntu.com trusty InRelease > > Ign http://archive.ubuntu.com precise InRelease > > [...] > > Then search for e.g. the "sickle" package in the repositories: > > > root at wildcat:~# apt search sickle > > Sorting... Done > > Full Text Search... Done > > r-cran-phtt/trusty 3.1.2-1cran1ppa0trusty0 all > > GNU R package "Panel Data Analysis with Heterogeneous Time > > > > sickle/trusty,now 1.33-1biolinux1 amd64 [installed] > > windowed adaptive trimming tool for FASTQ files using quality > > Having found that there is, indeed, a "sickle" package, you can show > details about the package and its dependencies: > > > root at wildcat:~# apt show sickle > > Package: sickle > > Priority: optional > > Section: science > > Installed-Size: 74.8 kB > > Maintainer: Debian Med Packaging Team < > debian-med-packaging at lists.alioth.debian.org> > > Version: 1.33-1biolinux1 > > Depends: libc6 (>= 2.14), zlib1g (>= 1:1.1.4) > > Download-Size: 17.3 kB > > APT-Manual-Installed: yes > > APT-Sources: http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ > trusty/main amd64 Packages > > Description: windowed adaptive trimming tool for FASTQ files using > quality > > Most modern sequencing technologies produce reads that have > deteriorating > > quality towards the 3'-end. Incorrectly called bases here negatively > impact > > assembles, mapping, and downstream bioinformatics analyses. > > . > > Sickle is a tool that uses sliding windows along with quality and length > > thresholds to determine when quality is sufficiently low to trim the > 3'-end > > of reads. It will also discard reads based upon the length threshold. > It takes > > the quality values and slides a window across them whose length is 0.1 > times > > the length of the read. If this length is less than 1, then the window > is set > > to be equal to the length of the read. Otherwise, the window slides > along the > > quality values until the average quality in the window drops below the > > threshold. At that point the algorithm determines where in the window > the drop > > occurs and cuts both the read and quality strings there. However, if > the cut > > point is less than the minimum length threshold, then the read is > discarded > > entirely. > > . > > Sickle supports four types of quality values: Illumina, Solexa, Phred, > and > > Sanger. Note that the Solexa quality setting is an approximation (the > actual > > conversion is a non-linear transformation). The end approximation is > close. > > . > > Sickle also supports gzipped file inputs. > > You can also see if other versions or upgrade candidates are available: > > > root at wildcat:~# apt-cache policy sickle > > sickle: > > Installed: 1.33-1biolinux1 > > Candidate: 1.33-1biolinux1 > > Version table: > > *** 1.33-1biolinux1 0 > > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main > amd64 Packages > > 100 /var/lib/dpkg/status > > 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 attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Sat Jun 11 08:53:50 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sat, 11 Jun 2016 13:53:50 +0100 Subject: [Bio-linux-list] Sickle biolinux 8 In-Reply-To: References: <575AF7DF.80809@minke-informatics.co.uk> Message-ID: <575C09DE.1030206@minke-informatics.co.uk> On 11/06/16 11:59, Flavia Flaviani wrote: > [...] > BUT in the last command I get this : > > ~$ apt-cache policy sickle > sickle: > Installed: (none) > Candidate: 1.33-1biolinux1 > Version table: > 1.33-1biolinux1 0 > 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ trusty/main > amd64 Packages > > > So it seems that it's there but not installed. Can you advise me on how > to fix this? Hi, Flavia. You can download and install the package from the repository using: sudo apt update sudo apt install sickle It's always best to update the APT database before you install new packages, to make sure that you get the latest version available. 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