From Christopher.Dubay at providence.org Tue Jan 6 14:36:26 2015 From: Christopher.Dubay at providence.org (Dubay, Christopher J) Date: Tue, 6 Jan 2015 19:36:26 +0000 Subject: [Bio-Linux] BioLinux 8 - Hangs after Login In-Reply-To: <548ED2E1.4050301@abdn.ac.uk> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> Message-ID: <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> On my first booting-up of BioLinux this year (2015), in a VMware under Windows 7 environment that had been working well, I was greeted with a new login screen image (green berries). Nice. I logged in, and never get to a working GUI (the same thing happens for the Guest account), I get a GUI window with no menus/icons (just green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart the GUI ('sudo service lightdm restart' just returns me to the GUI window with no menus/icons as before). I tried an 'sudo apt-get update', no joy. I am willing to try a reinstall, however I wanted to check with the community to see if this a Ubuntu or BioLinux problem. Seeing the login desktop image change just made me wonder; and I have never had a Ubuntu VM act this way. Has anyone else ever seen this behavior? Thanks, and Happy New Year... Christopher Christopher Dubay, PhD Biomedical Informatics Program Manager Laboratory of Molecular and Tumor Immunology Earle A. Chiles Research Institute Providence Cancer Center 4805 NE Glisan St.- 2N57 Portland, OR 97213 USA T: (503) 215-7981 F: (503) 215-6841 christopher.dubay at providence.org ________________________________ This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. From tbooth at ceh.ac.uk Wed Jan 7 05:26:12 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 7 Jan 2015 10:26:12 +0000 Subject: [Bio-Linux] BioLinux 8 - Hangs after Login In-Reply-To: <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> Message-ID: <1420626372.6251.60.camel@wllt1771.nerc-wallingford.ac.uk> Hi Christopher, I've seen a similar situation twice recently due to packages being inadvertently removed from the system. In the first case the user had wanted to install a Deb package file directly and got the message "this conflicts with existing packages - do you want to remove the conflicting packages?" So they did, and the desktop stopped working because they had removed essential desktop packages. In the second case, the user had an NVidia graphics card on their physical machine so they figured they would install the NVidia accelerated drivers under Linux to take advantage of it. Not only does this not work, but unfortunately the NVidia drivers break the VirtualBox drivers and then can't be removed without directly restoring some system files. This one was quite tricky to fix. Do you think you might have done anything like this on your own VM? The thing to appreciate is that the GUI on Linux is just a regular application that happens to stick itself to the side of the screen. You can try running it from the terminal by typing "unity" and see what it says - any informative errors? Ensure that the ubuntu-desktop package is still on your system as this meta-package depends on all the crucial desktop components like unity. Cheers, TIM On Tue, 2015-01-06 at 19:36 +0000, Dubay, Christopher J wrote: > On my first booting-up of BioLinux this year (2015), in a VMware under > Windows 7 environment that had been working well, I was greeted with a > new login screen image (green berries). Nice. > > I logged in, and never get to a working GUI (the same thing happens > for the Guest account), I get a GUI window with no menus/icons (just > green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart > the GUI ('sudo service lightdm restart' just returns me to the GUI > window with no menus/icons as before). > > I tried an 'sudo apt-get update', no joy. I am willing to try a > reinstall, however I wanted to check with the community to see if this > a Ubuntu or BioLinux problem. Seeing the login desktop image change > just made me wonder; and I have never had a Ubuntu VM act this way. > > Has anyone else ever seen this behavior? > > Thanks, and Happy New Year... > > Christopher > > > Christopher Dubay, PhD > Biomedical Informatics Program Manager > Laboratory of Molecular and Tumor Immunology > Earle A. Chiles Research Institute > Providence Cancer Center > 4805 NE Glisan St.- 2N57 > Portland, OR 97213 USA > T: (503) 215-7981 > F: (503) 215-6841 > > christopher.dubay at providence.org > > ________________________________ > > This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at abdn.ac.uk Wed Jan 7 05:35:41 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Wed, 7 Jan 2015 10:35:41 +0000 Subject: [Bio-Linux] BioLinux 8 - Hangs after Login In-Reply-To: <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> Message-ID: <54AD0BFD.3030100@abdn.ac.uk> On 06/01/15 19:36, Dubay, Christopher J wrote: > On my first booting-up of BioLinux this year (2015), in a VMware > under Windows 7 environment that had been working well, I was greeted > with a new login screen image (green berries). Nice. > > I logged in, and never get to a working GUI (the same thing happens > for the Guest account), I get a GUI window with no menus/icons (just > green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart > the GUI ('sudo service lightdm restart' just returns me to the GUI > window with no menus/icons as before). > [...] Hi, Christopher. You could try the Gnome 'Flashback' desktop instead or MATE, which does not require hardware accelerated graphics. I've found that you get a blank screen on a remote desktop (i.e. not a VM) if you try to run Unity and this is one reason why we use MATE as the remote desktop. Just select the icon to the upper right of where you type in your username on the login screen to choose a different desktop session. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From gawbul at gmail.com Wed Jan 7 07:12:00 2015 From: gawbul at gmail.com (Steve Moss) Date: Wed, 7 Jan 2015 12:12:00 +0000 Subject: [Bio-Linux] BioLinux 8 - Hangs after Login Message-ID: Dear Christopher, I've had a similar issue with my VirtualBox Bio-Linux8 installation recently, and haven't done any of the things that Tim suggested might be the cause. I have yet to investigate further, and have just been logging in via MATE instead to overcome the issue. Running sudo service lightdm restart from a terminal gets you back to the login screen where you can then choose MATE instead of GNOME. Cheers, Steve On 7 January 2015 at 12:00, wrote: > Message: 1 > Date: Tue, 6 Jan 2015 19:36:26 +0000 > From: "Dubay, Christopher J" > To: "bio-linux at nebclists.nerc.ac.uk" > Subject: [Bio-Linux] BioLinux 8 - Hangs after Login > Message-ID: > < > 3F9E65788480CD4282B12895264CC2143C244E9D at WN35105.or.providence.org> > Content-Type: text/plain; charset="us-ascii" > > On my first booting-up of BioLinux this year (2015), in a VMware under > Windows 7 environment that had been working well, I was greeted with a new > login screen image (green berries). Nice. > > I logged in, and never get to a working GUI (the same thing happens for > the Guest account), I get a GUI window with no menus/icons (just green > berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart the GUI > ('sudo service lightdm restart' just returns me to the GUI window with no > menus/icons as before). > > I tried an 'sudo apt-get update', no joy. I am willing to try a reinstall, > however I wanted to check with the community to see if this a Ubuntu or > BioLinux problem. Seeing the login desktop image change just made me > wonder; and I have never had a Ubuntu VM act this way. > > Has anyone else ever seen this behavior? > > Thanks, and Happy New Year... > > Christopher > > > Christopher Dubay, PhD > Biomedical Informatics Program Manager > Laboratory of Molecular and Tumor Immunology > Earle A. Chiles Research Institute > Providence Cancer Center > 4805 NE Glisan St.- 2N57 > Portland, OR 97213 USA > T: (503) 215-7981 > F: (503) 215-6841 > > christopher.dubay at providence.org > > ________________________________ > > This message is intended for the sole use of the addressee, and may > contain information that is privileged, confidential and exempt from > disclosure under applicable law. If you are not the addressee you are > hereby notified that you may not use, copy, disclose, or distribute to > anyone the message or any information contained in the message. If you have > received this message in error, please immediately advise the sender by > reply email and delete this message. > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Christopher.Dubay at providence.org Wed Jan 7 15:51:38 2015 From: Christopher.Dubay at providence.org (Dubay, Christopher J) Date: Wed, 7 Jan 2015 20:51:38 +0000 Subject: [Bio-Linux] BioLinux 8 - Hangs after Login In-Reply-To: <1420626372.6251.60.camel@wllt1771.nerc-wallingford.ac.uk> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> <1420626372.6251.60.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <3F9E65788480CD4282B12895264CC2143C245414@WN35105.or.providence.org> Thanks Tim, Tony, and Steve, Yes. Using MATE works for me. Neither the Ubuntu Default, or Gnome Flashback (either Compiz or Metacity) worked. Trying unity form the terminal gave an 'Error: plugin 'opengl' not loaded' in the startup (???). I have tried this with my VMware display settings as: 'host setting' and 'specified number of monitors' each with 3D graphics on and off. And still only MATE works for me. Previously to this issue, I did try doing an install of some Illumina software (bcl2fastq) which was a bit problematic (needed BOOST and other components), and ended up doing an RPM package install with alien. I am guessing that is where I screwed something up as Tim suggested by removing conflicting packages somewhere. I was ready to blame it on the new 'green berries'! At least I am back up again (albeit in MATE now). I am willing to do more troubleshooting of this. Tim: I could try 'sudo apt-get --reinstall ubuntu-desktop'; however I want to do a backup of the VM first. Other ideas? Thanks everyone! Christopher -----Original Message----- From: Tim Booth [mailto:tbooth at ceh.ac.uk] Sent: Wednesday, January 07, 2015 2:26 AM To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] BioLinux 8 - Hangs after Login Hi Christopher, I've seen a similar situation twice recently due to packages being inadvertently removed from the system. In the first case the user had wanted to install a Deb package file directly and got the message "this conflicts with existing packages - do you want to remove the conflicting packages?" So they did, and the desktop stopped working because they had removed essential desktop packages. In the second case, the user had an NVidia graphics card on their physical machine so they figured they would install the NVidia accelerated drivers under Linux to take advantage of it. Not only does this not work, but unfortunately the NVidia drivers break the VirtualBox drivers and then can't be removed without directly restoring some system files. This one was quite tricky to fix. Do you think you might have done anything like this on your own VM? The thing to appreciate is that the GUI on Linux is just a regular application that happens to stick itself to the side of the screen. You can try running it from the terminal by typing "unity" and see what it says - any informative errors? Ensure that the ubuntu-desktop package is still on your system as this meta-package depends on all the crucial desktop components like unity. Cheers, TIM On Tue, 2015-01-06 at 19:36 +0000, Dubay, Christopher J wrote: > On my first booting-up of BioLinux this year (2015), in a VMware under > Windows 7 environment that had been working well, I was greeted with a > new login screen image (green berries). Nice. > > I logged in, and never get to a working GUI (the same thing happens > for the Guest account), I get a GUI window with no menus/icons (just > green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart > the GUI ('sudo service lightdm restart' just returns me to the GUI > window with no menus/icons as before). > > I tried an 'sudo apt-get update', no joy. I am willing to try a > reinstall, however I wanted to check with the community to see if this > a Ubuntu or BioLinux problem. Seeing the login desktop image change > just made me wonder; and I have never had a Ubuntu VM act this way. > > Has anyone else ever seen this behavior? > > Thanks, and Happy New Year... > > Christopher > > > Christopher Dubay, PhD > Biomedical Informatics Program Manager Laboratory of Molecular and > Tumor Immunology Earle A. Chiles Research Institute Providence Cancer > Center > 4805 NE Glisan St.- 2N57 > Portland, OR 97213 USA > T: (503) 215-7981 > F: (503) 215-6841 > > christopher.dubay at providence.org > > ________________________________ > > This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux ________________________________ This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. From tbooth at ceh.ac.uk Thu Jan 8 05:20:41 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 8 Jan 2015 10:20:41 +0000 Subject: [Bio-Linux] BioLinux 8 on VirtualBox - Hangs after Login In-Reply-To: <3F9E65788480CD4282B12895264CC2143C245414@WN35105.or.providence.org> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> <1420626372.6251.60.camel@wllt1771.nerc-wallingford.ac.uk> <3F9E65788480CD4282B12895264CC2143C245414@WN35105.or.providence.org> Message-ID: <1420712441.6251.91.camel@wllt1771.nerc-wallingford.ac.uk> Hi Christopher, OK, this is bad. I've just tried booting up the VirtualBox version of Bio-Linux and applying all updates, and it breaks itself just as you describe. At the moment I do not know what is going wrong. I'll get back to the list as soon as I have a fix. In the meantime, I'd suggest that nobody using the VM version of Bio-Linux 8 applies any updates! Cheers, TIM On Wed, 2015-01-07 at 20:51 +0000, Dubay, Christopher J wrote: > Thanks Tim, Tony, and Steve, > > Yes. Using MATE works for me. Neither the Ubuntu Default, or Gnome Flashback (either Compiz or Metacity) worked. > > Trying unity form the terminal gave an 'Error: plugin 'opengl' not loaded' in the startup (???). > > I have tried this with my VMware display settings as: 'host setting' and 'specified number of monitors' each with 3D graphics on and off. And still only MATE works for me. > > Previously to this issue, I did try doing an install of some Illumina software (bcl2fastq) which was a bit problematic (needed BOOST and other components), and ended up doing an RPM package install with alien. I am guessing that is where I screwed something up as Tim suggested by removing conflicting packages somewhere. > > I was ready to blame it on the new 'green berries'! > > At least I am back up again (albeit in MATE now). > > I am willing to do more troubleshooting of this. Tim: I could try 'sudo apt-get --reinstall ubuntu-desktop'; however I want to do a backup of the VM first. Other ideas? > > Thanks everyone! > > Christopher > > > > -----Original Message----- > From: Tim Booth [mailto:tbooth at ceh.ac.uk] > Sent: Wednesday, January 07, 2015 2:26 AM > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] BioLinux 8 - Hangs after Login > > Hi Christopher, > > I've seen a similar situation twice recently due to packages being inadvertently removed from the system. In the first case the user had wanted to install a Deb package file directly and got the message "this conflicts with existing packages - do you want to remove the conflicting packages?" So they did, and the desktop stopped working because they had removed essential desktop packages. > > In the second case, the user had an NVidia graphics card on their physical machine so they figured they would install the NVidia accelerated drivers under Linux to take advantage of it. Not only does this not work, but unfortunately the NVidia drivers break the VirtualBox drivers and then can't be removed without directly restoring some system files. This one was quite tricky to fix. > > Do you think you might have done anything like this on your own VM? > > The thing to appreciate is that the GUI on Linux is just a regular application that happens to stick itself to the side of the screen. You can try running it from the terminal by typing "unity" and see what it says - any informative errors? Ensure that the ubuntu-desktop package is still on your system as this meta-package depends on all the crucial desktop components like unity. > > Cheers, > > TIM > > On Tue, 2015-01-06 at 19:36 +0000, Dubay, Christopher J wrote: > > On my first booting-up of BioLinux this year (2015), in a VMware under > > Windows 7 environment that had been working well, I was greeted with a > > new login screen image (green berries). Nice. > > > > I logged in, and never get to a working GUI (the same thing happens > > for the Guest account), I get a GUI window with no menus/icons (just > > green berries). I can Alt+Ctrl+F1 to a terminal, but cannot restart > > the GUI ('sudo service lightdm restart' just returns me to the GUI > > window with no menus/icons as before). > > > > I tried an 'sudo apt-get update', no joy. I am willing to try a > > reinstall, however I wanted to check with the community to see if this > > a Ubuntu or BioLinux problem. Seeing the login desktop image change > > just made me wonder; and I have never had a Ubuntu VM act this way. > > > > Has anyone else ever seen this behavior? > > > > Thanks, and Happy New Year... > > > > Christopher > > > > > > Christopher Dubay, PhD > > Biomedical Informatics Program Manager Laboratory of Molecular and > > Tumor Immunology Earle A. Chiles Research Institute Providence Cancer > > Center > > 4805 NE Glisan St.- 2N57 > > Portland, OR 97213 USA > > T: (503) 215-7981 > > F: (503) 215-6841 > > > > christopher.dubay at providence.org > > > > ________________________________ > > > > This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > ________________________________ > > This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tony.travis at abdn.ac.uk Thu Jan 8 05:59:36 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 8 Jan 2015 10:59:36 +0000 Subject: [Bio-Linux] BioLinux 8 on VirtualBox - Hangs after Login In-Reply-To: <1420712441.6251.91.camel@wllt1771.nerc-wallingford.ac.uk> References: <8C33D34D431A974EAEA913101DDA19440791420CF3@nerckwmbc.ad.nerc.ac.uk> <548ED2E1.4050301@abdn.ac.uk> <3F9E65788480CD4282B12895264CC2143C244E9D@WN35105.or.providence.org> <1420626372.6251.60.camel@wllt1771.nerc-wallingford.ac.uk> <3F9E65788480CD4282B12895264CC2143C245414@WN35105.or.providence.org> <1420712441.6251.91.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <54AE6318.5000500@abdn.ac.uk> On 08/01/15 10:20, Tim Booth wrote: > Hi Christopher, > > OK, this is bad. I've just tried booting up the VirtualBox version of > Bio-Linux and applying all updates, and it breaks itself just as you > describe. > > At the moment I do not know what is going wrong. I'll get back to the > list as soon as I have a fix. In the meantime, I'd suggest that nobody > using the VM version of Bio-Linux 8 applies any updates! Hi, Tim. I'd put my money on the known problems of Unity 2D and Gnome3 requiring hardware acceleration even it they don't actually use it and emulated VM graphics hardware not providing it. Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Fri Jan 9 06:45:48 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 9 Jan 2015 11:45:48 +0000 Subject: [Bio-Linux] Bio-Linux VirtualBox broken after updates - how to fix Message-ID: <1420803948.6251.171.camel@wllt1771.nerc-wallingford.ac.uk> Dear All, There is a driver update problem affecting Bio-Linux 8 for VirtualBox. If you apply the latest batch of updates via the update manager the VM will no longer boot to a working desktop. As far as I can tell this issue is limited to VirtualBox/VMWare, but I may be wrong. ** Symptoms: After rebooting the VM, you see the desktop wallpaper and nothing else. Or you may even just see a black screen. The system appears unresponsive but you can switch to a text terminal by holding down the Right Ctrl key and pressing F1 to get a text console login prompt. ** If you have already applied the problem updates and need to fix: 1. Switch to text console by holding down the Right Ctrl key and pressing F1 (or try Ctrl+Alt+F1 on Windows) 2. Log in - account is manager, password manager unless you changed it 3. $ sudo stop lightdm 4. $ startx -e mate-session 5. Now you should have some sort of usable desktop 6. Open a new terminal (ignore the XTerm window and don't close it) 7. $ sudo apt-get purge nvidia-331-updates nvidia-opencl-icd-331-updates nvidia-prime nvidia-settings libhwloc-plugins 8. $ sudo reboot That should do it! If, at this point, you just see your Desktop icons but no panel, get back in the text login and try this to reset your account settings: $ mkdir my_old_dot_files $ mv ~/.local ~/.g* my_old_dot_files/ $ sudo restart lightdm And that should really do it. ** If you have not yet applied the updates and want to avoid the problems, just remove two troublesome packages before updating: $ sudo apt-get purge nvidia-libopencl1-331-updates libhwloc-plugins You should see these two packages cleanly removed. I'm releasing an updated VirtualBox OVF image on the website today to address this problem. Apologies for this glitch - it's Ubuntu's fault, not mine, honest!! If you are still having problems or need clarification on the above please reply to the bio-linux at nebclists.nerc.ac.uk mailing list. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From kissaj at miamioh.edu Sat Jan 10 10:03:40 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Sat, 10 Jan 2015 10:03:40 -0500 Subject: [Bio-Linux] Install size of BL8? Message-ID: <1420902220.10159.40.camel@methy1> Hi Tim & All, What is the installed size of Bio-Linux 8 (14.04)? I have a separate 30 GB OS partition and wanted to make sure I have enough space before I upgrade and convert to Bio-Linux on this machine (currently on Ubuntu (non-Bio-Linux) 12.04.4 Thanks, -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.miamioh.edu/cbfg/ URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Sat Jan 10 18:07:37 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 10 Jan 2015 23:07:37 +0000 Subject: [Bio-Linux] Install size of BL8? In-Reply-To: <1420902220.10159.40.camel@methy1> References: <1420902220.10159.40.camel@methy1> Message-ID: <54B1B0B9.6010009@abdn.ac.uk> On 10/01/15 15:03, Andor J Kiss wrote: > Hi Tim & All, > > What is the installed size of Bio-Linux 8 (14.04)? I have a > separate 30 GB OS partition and wanted to make sure I have enough space > before I upgrade and convert to Bio-Linux on this machine (currently on > Ubuntu (non-Bio-Linux) 12.04.4 Hi, Andor. This is a recent install of Bio-Linux 8 onto an "md" RAID1+RAID6 on my workstation "polecat" (boot is on RAID1, everything else is on RAID6): > manager at polecat[manager] df -ht ext4 > Filesystem Size Used Avail Use% Mounted on > /dev/md1p1 333G 8.8G 307G 3% / > /dev/md1p4 916G 922M 868G 1% /home > /dev/md0p1 989M 92M 831M 10% /boot > /dev/md1p3 459G 950M 434G 1% /usr/local > /dev/md1p5 1.8T 68M 1.7T 1% /work Bear in mind that you can upgrade a 'standard' Ubuntu 12.04 LTS to Ubuntu 14.04 and Bio-Linux 8 in-place using Tim's upgrade script: http://environmentalomics.org/bio-linux-installation/ Look for "Upgrading Bio-Linux 7 (or Ubuntu) to Bio-Linux 8" I've done this upgrade on quite a few standard Ubuntu 12.04 and 14.04 systems as well as using the script to upgrade my Bio-Linux 7 systems. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From kissaj at miamioh.edu Sat Jan 10 23:48:27 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Sat, 10 Jan 2015 23:48:27 -0500 Subject: [Bio-Linux] Install size of BL8? In-Reply-To: <54B1B0B9.6010009@abdn.ac.uk> References: <1420902220.10159.40.camel@methy1> <54B1B0B9.6010009@abdn.ac.uk> Message-ID: <1420951707.10159.43.camel@methy1> Thanks! -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.miamioh.edu/cbfg/ URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss On Sat, 2015-01-10 at 23:07 +0000, Tony Travis wrote: > On 10/01/15 15:03, Andor J Kiss wrote: > > Hi Tim & All, > > > > What is the installed size of Bio-Linux 8 (14.04)? I have a > > separate 30 GB OS partition and wanted to make sure I have enough space > > before I upgrade and convert to Bio-Linux on this machine (currently on > > Ubuntu (non-Bio-Linux) 12.04.4 > > Hi, Andor. > > This is a recent install of Bio-Linux 8 onto an "md" RAID1+RAID6 on my > workstation "polecat" (boot is on RAID1, everything else is on RAID6): > > > manager at polecat[manager] df -ht ext4 > > Filesystem Size Used Avail Use% Mounted on > > /dev/md1p1 333G 8.8G 307G 3% / > > /dev/md1p4 916G 922M 868G 1% /home > > /dev/md0p1 989M 92M 831M 10% /boot > > /dev/md1p3 459G 950M 434G 1% /usr/local > > /dev/md1p5 1.8T 68M 1.7T 1% /work > > Bear in mind that you can upgrade a 'standard' Ubuntu 12.04 LTS to > Ubuntu 14.04 and Bio-Linux 8 in-place using Tim's upgrade script: > > http://environmentalomics.org/bio-linux-installation/ > > Look for "Upgrading Bio-Linux 7 (or Ubuntu) to Bio-Linux 8" > > I've done this upgrade on quite a few standard Ubuntu 12.04 and 14.04 > systems as well as using the script to upgrade my Bio-Linux 7 systems. > > HTH, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Mon Jan 12 05:57:27 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 12 Jan 2015 10:57:27 +0000 Subject: [Bio-Linux] Install size of BL8? In-Reply-To: <1420902220.10159.40.camel@methy1> References: <1420902220.10159.40.camel@methy1> Message-ID: <1421060247.6251.258.camel@wllt1771.nerc-wallingford.ac.uk> Hi Andor, 8.6 GB is the unpacked size. You'll need a little more that that in reality but 30GB is plenty assuming you have another disk to store your big data files. Cheers, TIM On Sat, 2015-01-10 at 15:03 +0000, Andor J Kiss wrote: > Hi Tim & All, > > What is the installed size of Bio-Linux 8 (14.04)? I have a > separate 30 GB OS partition and wanted to make sure I have enough > space before I upgrade and convert to Bio-Linux on this machine > (currently on Ubuntu (non-Bio-Linux) 12.04.4 > > Thanks, > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From kissaj at miamioh.edu Mon Jan 12 09:13:48 2015 From: kissaj at miamioh.edu (Andor J Kiss) Date: Mon, 12 Jan 2015 09:13:48 -0500 Subject: [Bio-Linux] Install size of BL8? In-Reply-To: <1421060247.6251.258.camel@wllt1771.nerc-wallingford.ac.uk> References: <1420902220.10159.40.camel@methy1> <1421060247.6251.258.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <1421072028.10159.50.camel@methy1> Hi Tim, Thanks. Is it a better strategy to upgrade the Ubuntu install from 12.04 to 14.04 and then convert to Bio-Linux, or better to convert to Bio-Linux and then upgrade from Bio-Linux 7 to Bio-Linux 8? Thanks, Andor On Mon, 2015-01-12 at 10:57 +0000, Tim Booth wrote: > Hi Andor, > > 8.6 GB is the unpacked size. You'll need a little more that that in > reality but 30GB is plenty assuming you have another disk to store your > big data files. > > Cheers, > > TIM > > On Sat, 2015-01-10 at 15:03 +0000, Andor J Kiss wrote: > > Hi Tim & All, > > > > What is the installed size of Bio-Linux 8 (14.04)? I have a > > separate 30 GB OS partition and wanted to make sure I have enough > > space before I upgrade and convert to Bio-Linux on this machine > > (currently on Ubuntu (non-Bio-Linux) 12.04.4 > > > > Thanks, > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Mon Jan 12 09:33:57 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 12 Jan 2015 14:33:57 +0000 Subject: [Bio-Linux] Install size of BL8? In-Reply-To: <1421072028.10159.50.camel@methy1> References: <1420902220.10159.40.camel@methy1> <1421060247.6251.258.camel@wllt1771.nerc-wallingford.ac.uk> <1421072028.10159.50.camel@methy1> Message-ID: <1421073237.29836.7.camel@wllt1771.nerc-wallingford.ac.uk> Hi Andor, The former, definitely. I don't think the script to install Bio-Linux 7 on Ubuntu 12.04 even works any more due to missing packages in the archive. Cheers, TIM On Mon, 2015-01-12 at 14:13 +0000, Andor J Kiss wrote: > Hi Tim, > > Thanks. Is it a better strategy to upgrade the Ubuntu install > from 12.04 to 14.04 and then convert to Bio-Linux, or better to > convert to Bio-Linux and then upgrade from Bio-Linux 7 to Bio-Linux 8? > > Thanks, > Andor > > On Mon, 2015-01-12 at 10:57 +0000, Tim Booth wrote: > > Hi Andor, > > > > 8.6 GB is the unpacked size. You'll need a little more that that in > > reality but 30GB is plenty assuming you have another disk to store your > > big data files. > > > > Cheers, > > > > TIM > > > > On Sat, 2015-01-10 at 15:03 +0000, Andor J Kiss wrote: > > > Hi Tim & All, > > > > > > What is the installed size of Bio-Linux 8 (14.04)? I have a > > > separate 30 GB OS partition and wanted to make sure I have enough > > > space before I upgrade and convert to Bio-Linux on this machine > > > (currently on Ubuntu (non-Bio-Linux) 12.04.4 > > > > > > Thanks, > > > > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Ian.Donaldson at manchester.ac.uk Fri Jan 16 05:45:52 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 16 Jan 2015 10:45:52 +0000 Subject: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk> Hi, I have followed the advice given in http://environmentalomics.org/bio-linux-galaxy/ and I have successfully set up the galaxy-server-apache-proxy. I have put a sam file (ex1.sam) in the transfer directory for manager at localhost and can see the file in the'Files uploaded via FTP' section. However, when I try to select and upload the file I get errors: >From the debug message: Traceback (most recent call last): File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, in __main__() File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, in __main__ add_file( dataset, registry, json_file, output_path ) File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line 116, in convert_newlines shutil.move( temp_name, fname ) File "/usr/lib/python2.7/shutil.py", line 302, in move copy2(src, real_dst) File "/usr/lib/python2.7/shutil.py", line 130, in copy2 copyfile(src, dst) File "/usr/lib/python2.7/shutil.py", line 83, in copyfile with open(dst, 'wb') as fdst: IOError: [Errno 13] Permission denied: u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam' >From the server.log: galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool upload1 created job id 2 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] "POST /galaxy/tool_runner/index HTTP/1.1" 200 - "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for job is: /usr/lib/galaxy-server/database/job_working_directory/000/2 galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to local runner 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing job script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external set_meta script for job 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of external set_meta for job 2 finished galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to ERROR galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up external metadata files 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" I noticed permission being mentioned. The status of the transfer directory is: drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost I change this to: drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost But the same thing happened. Has anyone seen this problem before and have and guidance? Thank you, Ian -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Fri Jan 16 06:12:38 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 16 Jan 2015 11:12:38 +0000 Subject: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory In-Reply-To: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk> Message-ID: <1421406758.2102.62.camel@wllt1771.nerc-wallingford.ac.uk> Hi Ian, The correct permission is: drwxrwx--- 2 user2 Debian-galaxy 4096 Feb 26 2014 user2 at localhost (or in your case, manager rather than user2) And anything else is going to cause problems. Galaxy on Bio-Linux is supposed to sort out the permissions when it starts up, but I had a couple of bugs in the old version of that startup script that could leave directories stuck with the wrong permissions. Would you mind trying deleting the manager at localhost directory entirely then restarting Galaxy. What permissions does it get recreated with? Cheers, TIM On Fri, 2015-01-16 at 10:45 +0000, Ian Donaldson wrote: > Hi, > > I have followed the advice given in > http://environmentalomics.org/bio-linux-galaxy/ and I have > successfully set up the galaxy-server-apache-proxy. I have put a sam > file (ex1.sam) in the transfer directory for manager at localhost and can > see the file in the'Files uploaded via FTP' section. However, when I > try to select and upload the file I get errors: > > From the debug message: > Traceback (most recent call last): > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, > in > __main__() > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, > in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, > in add_file > line_count, converted_path = sniff.convert_newlines( dataset.path, > in_place=in_place ) > File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line > 116, in convert_newlines > shutil.move( temp_name, fname ) > File "/usr/lib/python2.7/shutil.py", line 302, in move > copy2(src, real_dst) > File "/usr/lib/python2.7/shutil.py", line 130, in copy2 > copyfile(src, dst) > File "/usr/lib/python2.7/shutil.py", line 83, in copyfile > with open(dst, 'wb') as fdst: > IOError: [Errno 13] Permission denied: > u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam' > > > From the server.log: > galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool > upload1 created job id 2 > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > "POST /galaxy/tool_runner/index HTTP/1.1" 200 - > "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 > (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for > job is: /usr/lib/galaxy-server/database/job_working_directory/000/2 > galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to > local runner > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job > destination (destination id: local:///) > galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched > galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency > shell command for dependency 'samtools' > galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve > dependency on 'samtools', ignoring > galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: > python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing > job > script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job > destination (destination id: local:///) > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution > finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency > shell command for dependency 'samtools' > galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve > dependency on 'samtools', ignoring > galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external > set_meta script for job > 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII > galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of > external set_meta for job 2 finished > galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to > ERROR > galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended > galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up > external metadata files > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > > I noticed permission being mentioned. The status of the transfer > directory is: > drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost > > I change this to: > drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost > > But the same thing happened. > > Has anyone seen this problem before and have and guidance? > > Thank you, > Ian > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Ian.Donaldson at manchester.ac.uk Fri Jan 16 06:59:28 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 16 Jan 2015 11:59:28 +0000 Subject: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory In-Reply-To: <1421406758.2102.62.camel@wllt1771.nerc-wallingford.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk>, <1421406758.2102.62.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463AA8@MBXP02.ds.man.ac.uk> Thanks for your reply Tim. I deleted the directory and restarted GALAXY, the manager directory was recreated with the permissions you mention: drwxrwx--- 2 manager Debian-galaxy 4096 Jan 16 11:51 manager at localhost I can now input files! I am a bit confused about the groups though. 'Debian-galaxy' already exists, but 'galaxy' is mentioned in the instructions for setting up the FTP. Thanks again, Ian ________________________________________ From: Tim Booth [tbooth at ceh.ac.uk] Sent: 16 January 2015 11:12 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory Hi Ian, The correct permission is: drwxrwx--- 2 user2 Debian-galaxy 4096 Feb 26 2014 user2 at localhost (or in your case, manager rather than user2) And anything else is going to cause problems. Galaxy on Bio-Linux is supposed to sort out the permissions when it starts up, but I had a couple of bugs in the old version of that startup script that could leave directories stuck with the wrong permissions. Would you mind trying deleting the manager at localhost directory entirely then restarting Galaxy. What permissions does it get recreated with? Cheers, TIM On Fri, 2015-01-16 at 10:45 +0000, Ian Donaldson wrote: > Hi, > > I have followed the advice given in > http://environmentalomics.org/bio-linux-galaxy/ and I have > successfully set up the galaxy-server-apache-proxy. I have put a sam > file (ex1.sam) in the transfer directory for manager at localhost and can > see the file in the'Files uploaded via FTP' section. However, when I > try to select and upload the file I get errors: > > From the debug message: > Traceback (most recent call last): > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, > in > __main__() > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, > in __main__ > add_file( dataset, registry, json_file, output_path ) > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, > in add_file > line_count, converted_path = sniff.convert_newlines( dataset.path, > in_place=in_place ) > File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line > 116, in convert_newlines > shutil.move( temp_name, fname ) > File "/usr/lib/python2.7/shutil.py", line 302, in move > copy2(src, real_dst) > File "/usr/lib/python2.7/shutil.py", line 130, in copy2 > copyfile(src, dst) > File "/usr/lib/python2.7/shutil.py", line 83, in copyfile > with open(dst, 'wb') as fdst: > IOError: [Errno 13] Permission denied: > u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam' > > > From the server.log: > galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool > upload1 created job id 2 > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > "POST /galaxy/tool_runner/index HTTP/1.1" 200 - > "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 > (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for > job is: /usr/lib/galaxy-server/database/job_working_directory/000/2 > galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to > local runner > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job > destination (destination id: local:///) > galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched > galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency > shell command for dependency 'samtools' > galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve > dependency on 'samtools', ignoring > galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: > python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing > job > script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job > destination (destination id: local:///) > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution > finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency > shell command for dependency 'samtools' > galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve > dependency on 'samtools', ignoring > galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external > set_meta script for job > 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII > galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of > external set_meta for job 2 finished > galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to > ERROR > galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended > galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up > external metadata files > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > > I noticed permission being mentioned. The status of the transfer > directory is: > drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost > > I change this to: > drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost > > But the same thing happened. > > Has anyone seen this problem before and have and guidance? > > Thank you, > Ian > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Fri Jan 16 09:24:14 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 16 Jan 2015 14:24:14 +0000 Subject: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory In-Reply-To: <7E756F18289AF64B967C333AC3BF7021017C463AA8@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk> , <1421406758.2102.62.camel@wllt1771.nerc-wallingford.ac.uk> <7E756F18289AF64B967C333AC3BF7021017C463AA8@MBXP02.ds.man.ac.uk> Message-ID: <1421418254.14602.12.camel@wllt1771.nerc-wallingford.ac.uk> Hi Ian, It's a bit subtle - galaxy is the group for regular users who can use Galaxy eg. manager is in group galaxy Debian-galaxy is a group just for the GALAXY server process, which runs under a system user account named Debian-galaxy. It allows me to say that the manager at localhost directory is visible and writeable for the manager user and also the GALAXY server but closed to everyone else. No other users should be added to the Debian-galaxy group and furthermore the Debian-galaxy user should not be a member of the regular galaxy group. Clear as mud? If you still think there's a typo in my on-line instructions then let me know which bit you are looking at and I'll try to fix/clarify it. TIM On Fri, 2015-01-16 at 11:59 +0000, Ian Donaldson wrote: > Thanks for your reply Tim. > > I deleted the directory and restarted GALAXY, the manager directory was recreated with the permissions you mention: > drwxrwx--- 2 manager Debian-galaxy 4096 Jan 16 11:51 manager at localhost > > I can now input files! > > I am a bit confused about the groups though. 'Debian-galaxy' already exists, but 'galaxy' is mentioned in the instructions for setting up the FTP. > > Thanks again, > Ian > > ________________________________________ > From: Tim Booth [tbooth at ceh.ac.uk] > Sent: 16 January 2015 11:12 > To: bio-linux at nebclists.nerc.ac.uk > Subject: Re: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory > > Hi Ian, > > The correct permission is: > > drwxrwx--- 2 user2 Debian-galaxy 4096 Feb 26 2014 user2 at localhost > (or in your case, manager rather than user2) > > And anything else is going to cause problems. Galaxy on Bio-Linux is > supposed to sort out the permissions when it starts up, but I had a > couple of bugs in the old version of that startup script that could > leave directories stuck with the wrong permissions. Would you mind > trying deleting the manager at localhost directory entirely then restarting > Galaxy. What permissions does it get recreated with? > > Cheers, > > TIM > > On Fri, 2015-01-16 at 10:45 +0000, Ian Donaldson wrote: > > Hi, > > > > I have followed the advice given in > > http://environmentalomics.org/bio-linux-galaxy/ and I have > > successfully set up the galaxy-server-apache-proxy. I have put a sam > > file (ex1.sam) in the transfer directory for manager at localhost and can > > see the file in the'Files uploaded via FTP' section. However, when I > > try to select and upload the file I get errors: > > > > From the debug message: > > Traceback (most recent call last): > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, > > in > > __main__() > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, > > in __main__ > > add_file( dataset, registry, json_file, output_path ) > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, > > in add_file > > line_count, converted_path = sniff.convert_newlines( dataset.path, > > in_place=in_place ) > > File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line > > 116, in convert_newlines > > shutil.move( temp_name, fname ) > > File "/usr/lib/python2.7/shutil.py", line 302, in move > > copy2(src, real_dst) > > File "/usr/lib/python2.7/shutil.py", line 130, in copy2 > > copyfile(src, dst) > > File "/usr/lib/python2.7/shutil.py", line 83, in copyfile > > with open(dst, 'wb') as fdst: > > IOError: [Errno 13] Permission denied: > > u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam' > > > > > > From the server.log: > > galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool > > upload1 created job id 2 > > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > > "POST /galaxy/tool_runner/index HTTP/1.1" 200 - > > "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 > > (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for > > job is: /usr/lib/galaxy-server/database/job_working_directory/000/2 > > galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to > > local runner > > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job > > destination (destination id: local:///) > > galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched > > galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency > > shell command for dependency 'samtools' > > galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve > > dependency on 'samtools', ignoring > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: > > python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat > > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing > > job > > script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > > galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job > > destination (destination id: local:///) > > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution > > finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > > galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency > > shell command for dependency 'samtools' > > galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve > > dependency on 'samtools', ignoring > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external > > set_meta script for job > > 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of > > external set_meta for job 2 finished > > galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to > > ERROR > > galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended > > galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up > > external metadata files > > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > > > > > I noticed permission being mentioned. The status of the transfer > > directory is: > > drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost > > > > I change this to: > > drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost > > > > But the same thing happened. > > > > Has anyone seen this problem before and have and guidance? > > > > Thank you, > > Ian > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://environmentalomics.org/bio-linux > +44 1491 69 2297 > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Ian.Donaldson at manchester.ac.uk Fri Jan 16 09:44:40 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 16 Jan 2015 14:44:40 +0000 Subject: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory In-Reply-To: <1421418254.14602.12.camel@wllt1771.nerc-wallingford.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463A8E@MBXP02.ds.man.ac.uk> , <1421406758.2102.62.camel@wllt1771.nerc-wallingford.ac.uk> <7E756F18289AF64B967C333AC3BF7021017C463AA8@MBXP02.ds.man.ac.uk>, <1421418254.14602.12.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463AF8@MBXP02.ds.man.ac.uk> Thanks again for the explanation. I don't think there is a typo, you have explained why there are two galaxy groups. Very helpful! Ian ________________________________________ From: Tim Booth [tbooth at ceh.ac.uk] Sent: 16 January 2015 14:24 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory Hi Ian, It's a bit subtle - galaxy is the group for regular users who can use Galaxy eg. manager is in group galaxy Debian-galaxy is a group just for the GALAXY server process, which runs under a system user account named Debian-galaxy. It allows me to say that the manager at localhost directory is visible and writeable for the manager user and also the GALAXY server but closed to everyone else. No other users should be added to the Debian-galaxy group and furthermore the Debian-galaxy user should not be a member of the regular galaxy group. Clear as mud? If you still think there's a typo in my on-line instructions then let me know which bit you are looking at and I'll try to fix/clarify it. TIM On Fri, 2015-01-16 at 11:59 +0000, Ian Donaldson wrote: > Thanks for your reply Tim. > > I deleted the directory and restarted GALAXY, the manager directory was recreated with the permissions you mention: > drwxrwx--- 2 manager Debian-galaxy 4096 Jan 16 11:51 manager at localhost > > I can now input files! > > I am a bit confused about the groups though. 'Debian-galaxy' already exists, but 'galaxy' is mentioned in the instructions for setting up the FTP. > > Thanks again, > Ian > > ________________________________________ > From: Tim Booth [tbooth at ceh.ac.uk] > Sent: 16 January 2015 11:12 > To: bio-linux at nebclists.nerc.ac.uk > Subject: Re: [Bio-Linux] Problem with adding data to GALAXY using FTP upload via transfer directory > > Hi Ian, > > The correct permission is: > > drwxrwx--- 2 user2 Debian-galaxy 4096 Feb 26 2014 user2 at localhost > (or in your case, manager rather than user2) > > And anything else is going to cause problems. Galaxy on Bio-Linux is > supposed to sort out the permissions when it starts up, but I had a > couple of bugs in the old version of that startup script that could > leave directories stuck with the wrong permissions. Would you mind > trying deleting the manager at localhost directory entirely then restarting > Galaxy. What permissions does it get recreated with? > > Cheers, > > TIM > > On Fri, 2015-01-16 at 10:45 +0000, Ian Donaldson wrote: > > Hi, > > > > I have followed the advice given in > > http://environmentalomics.org/bio-linux-galaxy/ and I have > > successfully set up the galaxy-server-apache-proxy. I have put a sam > > file (ex1.sam) in the transfer directory for manager at localhost and can > > see the file in the'Files uploaded via FTP' section. However, when I > > try to select and upload the file I get errors: > > > > From the debug message: > > Traceback (most recent call last): > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 394, > > in > > __main__() > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 383, > > in __main__ > > add_file( dataset, registry, json_file, output_path ) > > File "/usr/lib/galaxy-server/tools/data_source/upload.py", line 278, > > in add_file > > line_count, converted_path = sniff.convert_newlines( dataset.path, > > in_place=in_place ) > > File "/usr/lib/galaxy-server/lib/galaxy/datatypes/sniff.py", line > > 116, in convert_newlines > > shutil.move( temp_name, fname ) > > File "/usr/lib/python2.7/shutil.py", line 302, in move > > copy2(src, real_dst) > > File "/usr/lib/python2.7/shutil.py", line 130, in copy2 > > copyfile(src, dst) > > File "/usr/lib/python2.7/shutil.py", line 83, in copyfile > > with open(dst, 'wb') as fdst: > > IOError: [Errno 13] Permission denied: > > u'/var/lib/galaxy-server/transfer/manager at localhost/ex1.sam' > > > > > > From the server.log: > > galaxy.tools.actions.upload_common INFO 2015-01-16 10:35:07,359 tool > > upload1 created job id 2 > > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > > "POST /galaxy/tool_runner/index HTTP/1.1" 200 - > > "http://localhost/galaxy/tool_runner?tool_id=upload1" "Mozilla/5.0 > > (X11; Ubuntu; Linux x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > galaxy.jobs DEBUG 2015-01-16 10:35:07,485 (2) Working directory for > > job is: /usr/lib/galaxy-server/database/job_working_directory/000/2 > > galaxy.jobs.handler DEBUG 2015-01-16 10:35:07,496 (2) Dispatching to > > local runner > > 127.0.0.1 - - [16/Jan/2015:10:35:07 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > galaxy.jobs DEBUG 2015-01-16 10:35:07,599 (2) Persisting job > > destination (destination id: local:///) > > galaxy.jobs.handler INFO 2015-01-16 10:35:07,622 (2) Job dispatched > > galaxy.tools.deps DEBUG 2015-01-16 10:35:07,770 Building dependency > > shell command for dependency 'samtools' > > galaxy.tools.deps WARNING 2015-01-16 10:35:07,770 Failed to resolve > > dependency on 'samtools', ignoring > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:07,833 (2) command is: > > python /usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/tmp/tmp9nLfry 2:/usr/lib/galaxy-server/database/job_working_directory/000/2/dataset_2_files:/usr/lib/galaxy-server/database/files/000/dataset_2.dat > > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:07,834 (2) executing > > job > > script: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > > galaxy.jobs DEBUG 2015-01-16 10:35:07,862 (2) Persisting job > > destination (destination id: local:///) > > galaxy.jobs.runners.local DEBUG 2015-01-16 10:35:08,617 execution > > finished: /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy_2.sh > > galaxy.tools.deps DEBUG 2015-01-16 10:35:08,684 Building dependency > > shell command for dependency 'samtools' > > galaxy.tools.deps WARNING 2015-01-16 10:35:08,684 Failed to resolve > > dependency on 'samtools', ignoring > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:08,684 executing external > > set_meta script for job > > 2: /usr/lib/galaxy-server/set_metadata.sh ./database/files /usr/lib/galaxy-server/database/job_working_directory/000/2 . /tmp/universe_wsgi_jymQ.ini /usr/lib/galaxy-server/database/tmp/tmp7LWfBs /usr/lib/galaxy-server/database/job_working_directory/000/2/galaxy.json /usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_eqLSN4,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_Y8KWCA,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_e8sRbx,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_s439LW,,/usr/lib/galaxy-server/database/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_jlOhII > > galaxy.jobs.runners DEBUG 2015-01-16 10:35:09,731 execution of > > external set_meta for job 2 finished > > galaxy.jobs DEBUG 2015-01-16 10:35:09,789 setting dataset state to > > ERROR > > galaxy.jobs DEBUG 2015-01-16 10:35:09,874 job 2 ended > > galaxy.datatypes.metadata DEBUG 2015-01-16 10:35:09,874 Cleaning up > > external metadata files > > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891/contents HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > 127.0.0.1 - - [16/Jan/2015:10:35:11 +0000] > > "GET /galaxy/api/histories/1cd8e2f6b131e891 HTTP/1.1" 200 - > > "http://localhost/galaxy/root/index" "Mozilla/5.0 (X11; Ubuntu; Linux > > x86_64; rv:34.0) Gecko/20100101 Firefox/34.0" > > > > > > I noticed permission being mentioned. The status of the transfer > > directory is: > > drwxr-xr-x 2 root root 4096 Jan 16 10:12 manager at localhost > > > > I change this to: > > drwxr-xr-x 2 manager manager 4096 Jan 16 10:12 manager at localhost > > > > But the same thing happened. > > > > Has anyone seen this problem before and have and guidance? > > > > Thank you, > > Ian > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://environmentalomics.org/bio-linux > +44 1491 69 2297 > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From Ian.Donaldson at manchester.ac.uk Fri Jan 16 11:11:34 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 16 Jan 2015 16:11:34 +0000 Subject: [Bio-Linux] GALAXY import file size limit? Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk> Hi, I am trying out Bio-Linux 8 using the VM download. I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out. Can anyone recommend a usable amount of RAM to allow this sort of operation to complete? My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial. Thank you, Ian From sgrannem at staffmail.ed.ac.uk Fri Jan 16 11:29:12 2015 From: sgrannem at staffmail.ed.ac.uk (Sander Granneman) Date: Fri, 16 Jan 2015 16:29:12 +0000 Subject: [Bio-Linux] GALAXY import file size limit? In-Reply-To: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk> Message-ID: <02CC0CD7-3923-4E32-BA24-1900D8999010@staffmail.ed.ac.uk> Simplest solution I guess is to use smaller bed files. 1.5 GB I guess equates to 10 million reads? Would 1 million suffice for your tutorial? Hope this helps, Sander > On Jan 16, 2015, at 4:11 PM, Ian Donaldson wrote: > > Hi, > > I am trying out Bio-Linux 8 using the VM download. I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out. Can anyone recommend a usable amount of RAM to allow this sort of operation to complete? > > My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial. > > Thank you, > > Ian > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > ------------------------------------------------------------------ -------- !!! Book the dates !!! The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). -------- Sander Granneman, PhD Wellcome Trust RCD Fellow University of Edinburgh Institute of Structural and Molecular Biology Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh Phone: office: +44 (0) 131 651 9082 lab: +44 (0) 131 651 9055 sgrannem at staffmail.ed.ac.uk http://sandergranneman.bio.ed.ac.uk http://www.csbe.ed.ac.uk/ ------------------------------------------------------------------ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From Ian.Donaldson at manchester.ac.uk Mon Jan 19 03:56:45 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Mon, 19 Jan 2015 08:56:45 +0000 Subject: [Bio-Linux] GALAXY import file size limit? In-Reply-To: <02CC0CD7-3923-4E32-BA24-1900D8999010@staffmail.ed.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk>, <02CC0CD7-3923-4E32-BA24-1900D8999010@staffmail.ed.ac.uk> Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463C0B@MBXP02.ds.man.ac.uk> Thank you for your reply. The aim was that people could also run their own analysis using the same VM. Is it fair to say that the VM option is not suitable for "real world" analysis, in favour of a full install? Ian ________________________________________ From: Sander Granneman [sgrannem at staffmail.ed.ac.uk] Sent: 16 January 2015 16:29 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] GALAXY import file size limit? Simplest solution I guess is to use smaller bed files. 1.5 GB I guess equates to 10 million reads? Would 1 million suffice for your tutorial? Hope this helps, Sander > On Jan 16, 2015, at 4:11 PM, Ian Donaldson wrote: > > Hi, > > I am trying out Bio-Linux 8 using the VM download. I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out. Can anyone recommend a usable amount of RAM to allow this sort of operation to complete? > > My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial. > > Thank you, > > Ian > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > ------------------------------------------------------------------ -------- !!! Book the dates !!! The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). -------- Sander Granneman, PhD Wellcome Trust RCD Fellow University of Edinburgh Institute of Structural and Molecular Biology Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh Phone: office: +44 (0) 131 651 9082 lab: +44 (0) 131 651 9055 sgrannem at staffmail.ed.ac.uk http://sandergranneman.bio.ed.ac.uk http://www.csbe.ed.ac.uk/ ------------------------------------------------------------------ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From sgrannem at staffmail.ed.ac.uk Mon Jan 19 04:22:11 2015 From: sgrannem at staffmail.ed.ac.uk (Sander Granneman) Date: Mon, 19 Jan 2015 09:22:11 +0000 Subject: [Bio-Linux] GALAXY import file size limit? In-Reply-To: <7E756F18289AF64B967C333AC3BF7021017C463C0B@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk> <, > <02CC0CD7-3923-4E32-BA24-1900D8999010@staffmail.ed.ac.uk> <7E756F18289AF64B967C333AC3BF7021017C463C0B@MBXP02.ds.man.ac.uk> Message-ID: <8E839591-6467-46CD-B759-C5E3F711E1E4@staffmail.ed.ac.uk> Hi Ian, I guess it all depends on what organism/kind of data they are analyzing and what kind of machine you have. A VM works just fine but RAM (and perhaps no of cpus) will likely be a limiting factor. Our analyses are mostly done on only a few million reads (CLIP) and sometimes we don?t need more than 4GB of RAM. But I would guess you would need at least 16GB of RAM if you want to do any serious analyses on mouse/human data. For a Galaxy tutorial I guess a VM should be fine. Also if they want to use the VM to do analyses on their own machine, they could always bump up the RAM for the VM? Sander > On Jan 19, 2015, at 8:56 AM, Ian Donaldson wrote: > > Thank you for your reply. The aim was that people could also run their own analysis using the same VM. Is it fair to say that the VM option is not suitable for "real world" analysis, in favour of a full install? > > Ian > > ________________________________________ > From: Sander Granneman [sgrannem at staffmail.ed.ac.uk] > Sent: 16 January 2015 16:29 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] GALAXY import file size limit? > > Simplest solution I guess is to use smaller bed files. > 1.5 GB I guess equates to 10 million reads? > Would 1 million suffice for your tutorial? > > Hope this helps, > > Sander > >> On Jan 16, 2015, at 4:11 PM, Ian Donaldson wrote: >> >> Hi, >> >> I am trying out Bio-Linux 8 using the VM download. I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out. Can anyone recommend a usable amount of RAM to allow this sort of operation to complete? >> >> My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial. >> >> Thank you, >> >> Ian >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> > > ------------------------------------------------------------------ > -------- > > !!! Book the dates !!! > > The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. > > Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). > > -------- > > Sander Granneman, PhD > Wellcome Trust RCD Fellow > University of Edinburgh > Institute of Structural and Molecular Biology > Centre for Synthetic and Systems Biology (SynthSys) > University of Edinburgh > Max Born Crescent > CH Waddington Building, room 3.06 > EH9 3BF > Edinburgh > > Phone: > office: +44 (0) 131 651 9082 > lab: +44 (0) 131 651 9055 > > sgrannem at staffmail.ed.ac.uk > > http://sandergranneman.bio.ed.ac.uk > http://www.csbe.ed.ac.uk/ > ------------------------------------------------------------------ > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > ------------------------------------------------------------------ -------- !!! Book the dates !!! The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). -------- Sander Granneman, PhD Wellcome Trust RCD Fellow University of Edinburgh Institute of Structural and Molecular Biology Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh Phone: office: +44 (0) 131 651 9082 lab: +44 (0) 131 651 9055 sgrannem at staffmail.ed.ac.uk http://sandergranneman.bio.ed.ac.uk http://www.csbe.ed.ac.uk/ ------------------------------------------------------------------ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From Ian.Donaldson at manchester.ac.uk Mon Jan 19 04:45:12 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Mon, 19 Jan 2015 09:45:12 +0000 Subject: [Bio-Linux] GALAXY import file size limit? In-Reply-To: <8E839591-6467-46CD-B759-C5E3F711E1E4@staffmail.ed.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C463B1D@MBXP02.ds.man.ac.uk> <, > <02CC0CD7-3923-4E32-BA24-1900D8999010@staffmail.ed.ac.uk> <7E756F18289AF64B967C333AC3BF7021017C463C0B@MBXP02.ds.man.ac.uk>, <8E839591-6467-46CD-B759-C5E3F711E1E4@staffmail.ed.ac.uk> Message-ID: <7E756F18289AF64B967C333AC3BF7021017C463C35@MBXP02.ds.man.ac.uk> Thanks for your input! Ian ________________________________________ From: Sander Granneman [sgrannem at staffmail.ed.ac.uk] Sent: 19 January 2015 09:22 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] GALAXY import file size limit? Hi Ian, I guess it all depends on what organism/kind of data they are analyzing and what kind of machine you have. A VM works just fine but RAM (and perhaps no of cpus) will likely be a limiting factor. Our analyses are mostly done on only a few million reads (CLIP) and sometimes we don?t need more than 4GB of RAM. But I would guess you would need at least 16GB of RAM if you want to do any serious analyses on mouse/human data. For a Galaxy tutorial I guess a VM should be fine. Also if they want to use the VM to do analyses on their own machine, they could always bump up the RAM for the VM? Sander > On Jan 19, 2015, at 8:56 AM, Ian Donaldson wrote: > > Thank you for your reply. The aim was that people could also run their own analysis using the same VM. Is it fair to say that the VM option is not suitable for "real world" analysis, in favour of a full install? > > Ian > > ________________________________________ > From: Sander Granneman [sgrannem at staffmail.ed.ac.uk] > Sent: 16 January 2015 16:29 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] GALAXY import file size limit? > > Simplest solution I guess is to use smaller bed files. > 1.5 GB I guess equates to 10 million reads? > Would 1 million suffice for your tutorial? > > Hope this helps, > > Sander > >> On Jan 16, 2015, at 4:11 PM, Ian Donaldson wrote: >> >> Hi, >> >> I am trying out Bio-Linux 8 using the VM download. I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out. Can anyone recommend a usable amount of RAM to allow this sort of operation to complete? >> >> My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial. >> >> Thank you, >> >> Ian >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux >> > > ------------------------------------------------------------------ > -------- > > !!! Book the dates !!! > > The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. > > Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). > > -------- > > Sander Granneman, PhD > Wellcome Trust RCD Fellow > University of Edinburgh > Institute of Structural and Molecular Biology > Centre for Synthetic and Systems Biology (SynthSys) > University of Edinburgh > Max Born Crescent > CH Waddington Building, room 3.06 > EH9 3BF > Edinburgh > > Phone: > office: +44 (0) 131 651 9082 > lab: +44 (0) 131 651 9055 > > sgrannem at staffmail.ed.ac.uk > > http://sandergranneman.bio.ed.ac.uk > http://www.csbe.ed.ac.uk/ > ------------------------------------------------------------------ > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > ------------------------------------------------------------------ -------- !!! Book the dates !!! The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015. Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee). -------- Sander Granneman, PhD Wellcome Trust RCD Fellow University of Edinburgh Institute of Structural and Molecular Biology Centre for Synthetic and Systems Biology (SynthSys) University of Edinburgh Max Born Crescent CH Waddington Building, room 3.06 EH9 3BF Edinburgh Phone: office: +44 (0) 131 651 9082 lab: +44 (0) 131 651 9055 sgrannem at staffmail.ed.ac.uk http://sandergranneman.bio.ed.ac.uk http://www.csbe.ed.ac.uk/ ------------------------------------------------------------------ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Fri Jan 23 09:39:59 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 23 Jan 2015 14:39:59 +0000 Subject: [Bio-Linux] Stacks RAD-seq software on Bio-Linux Message-ID: <1422023999.13659.52.camel@wllt1771.nerc-wallingford.ac.uk> Hi All, A very long time ago, someone asked me if I could put Stacks (http://creskolab.uoregon.edu/stacks/) on Bio-Linux. More recently, other people have asked more insistently if I can do a package, and I finally have. So you can "apt-get install stacks" then type: $ stacks help To see available commands. There are various problems with getting Stacks to work well as a package, especially the database and web viewer bit, which I've split into a package called "stacks-web". The standard installation is both really complex and assumes that you are the sole user on the system, or at least that you don't care about other users accessing all your stuff. I think I've made things much neater and simpler, but the upshot is that most of the regular set-up instructions are misleading for anyone using this new package. Essentially there is now just one thing to do - running: $ sudo stacks-setup-database Before that particular user tries to load anything to the database. If you are interested in using Stacks please let me know if you try these packages, and let me know if they actually work or if you have any problems/questions. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Ian.Donaldson at manchester.ac.uk Fri Jan 23 10:11:21 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 23 Jan 2015 15:11:21 +0000 Subject: [Bio-Linux] Bio-Linux 8 - GALAXY missing genome versions Message-ID: <7E756F18289AF64B967C333AC3BF7021017C464038@MBXP02.ds.man.ac.uk> Would it be possible to add 'mm10' and 'hg38' as genome builds within GALAXY. Specifically I mean GALAXY does not have an option for these genome builds in the drop down menu for new data. Or perhaps there is a easy way of adding them as admin? Thanks, Ian From suzanneluziagomes at gmail.com Mon Jan 26 11:06:50 2015 From: suzanneluziagomes at gmail.com (Suzanne Gomes) Date: Mon, 26 Jan 2015 10:06:50 -0600 Subject: [Bio-Linux] Problems with Tophat Message-ID: <6F8C8A79-B7A3-4785-9CA8-23ADBBB93B08@gmail.com> Hi! Brand new biolinux user here, and not really a computer person. My lab recently got a machine running biolinux 8 so we could do analysis with Galaxy. However I am having problems running Tophat and Tophat2. The first issue is with Tophat2, which gives the following error message: Fatal error: Tool execution failed Building a SMALL index [2015-01-19 12:10:58] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-01-19 12:10:58] Checking for Bowtie Bowtie 2 not found, checking for older version.. Bowtie version: 1.0.1.0 [2015-01-19 12:10:58] Checking for Samtools Samtools version: 0.1.19.0 [2015-01-19 12:10:58] Checking for Bowtie index files (genome).. Error: Could not find Bowtie index files (genome.*.ebwt) I read something in the mailing list from December that mentioned a problem with Tophat and bowtie not interacting properly, but it sounded as if that had been resolved. However, I think the install of biolinux on our computer was from before that fix (we had the install on a memory stick for a while before the computer was actually ready to go). But I am under the impression that biolinux automatically updates, so the fix should have been implemented after we installed, right? I?m not sure how to check if updates are installing. The second issue is with Tophat (which I tried after Tophat2 failed), which gives this error message: Error in tophat: tophat: option --no-closure-search not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html This error happens both with closure search turned on and turned off. Any suggestions for resolving these issues would be really appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Mon Jan 26 11:27:10 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 26 Jan 2015 16:27:10 +0000 Subject: [Bio-Linux] Problems with Tophat In-Reply-To: <6F8C8A79-B7A3-4785-9CA8-23ADBBB93B08@gmail.com> References: <6F8C8A79-B7A3-4785-9CA8-23ADBBB93B08@gmail.com> Message-ID: <1422289630.13659.145.camel@wllt1771.nerc-wallingford.ac.uk> Hi Suzanne, The first thing to note is that Tophat and Tophat2 are actually the same program. (Unlike Bowtie and Bowtie2 which are different) The second thing I noticed is you have Tophat 2.0.9 so this is definitely out-of-date. To check and install updates ensure you are logged in as a user with "sudo" privileges and then start the Software Updater. To find that, click on the swirly icon at the top left of your screen and then type "update" into the search box. This should bring up the relevant icon and guide you through the rest. If you are only running in the terminal, or if the graphical updater gives you errors, then you can do it this way: $ sudo apt-get update $ sudo apt-get dist-upgrade Let me know if that works/helps. In general, we can't do fully transparent updates of all software so you do need to check every so often and accept new updates. Cheers, TIM On Mon, 2015-01-26 at 16:06 +0000, Suzanne Gomes wrote: > Hi! > > > > Brand new biolinux user here, and not really a computer person. My lab > recently got a machine running biolinux 8 so we could do analysis with > Galaxy. However I am having problems running Tophat and Tophat2. > > > > The first issue is with Tophat2, which gives the following error > message: > > > > Fatal error: Tool execution failed > > Building a SMALL index > > > > [2015-01-19 12:10:58] Beginning TopHat run (v2.0.9) > > ----------------------------------------------- > > [2015-01-19 12:10:58] Checking for Bowtie > > Bowtie 2 not found, checking for older version.. > > Bowtie version: 1.0.1.0 > > [2015-01-19 12:10:58] Checking for Samtools > > Samtools version: 0.1.19.0 > > [2015-01-19 12:10:58] Checking for Bowtie index files (genome).. > > Error: Could not find Bowtie index files (genome.*.ebwt) > > > > I read something in the mailing list from December that mentioned a > problem with Tophat and bowtie not interacting properly, but it > sounded as if that had been resolved. However, I think the install of > biolinux on our computer was from before that fix (we had the install > on a memory stick for a while before the computer was actually ready > to go). But I am under the impression that biolinux automatically > updates, so the fix should have been implemented after we installed, > right? I?m not sure how to check if updates are installing. > > > > The second issue is with Tophat (which I tried after Tophat2 failed), > which gives this error message: > > > > Error in tophat: > > tophat: option --no-closure-search not recognized > > for detailed help see http://tophat.cbcb.umd.edu/manual.html > > > > This error happens both with closure search turned on and turned off. > > > Any suggestions for resolving these issues would be really > appreciated. > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From Sejal.Modha at glasgow.ac.uk Mon Jan 26 11:32:30 2015 From: Sejal.Modha at glasgow.ac.uk (Sejal Modha) Date: Mon, 26 Jan 2015 16:32:30 +0000 Subject: [Bio-Linux] Problems with Tophat In-Reply-To: <6F8C8A79-B7A3-4785-9CA8-23ADBBB93B08@gmail.com> References: <6F8C8A79-B7A3-4785-9CA8-23ADBBB93B08@gmail.com> Message-ID: <92A06C52-A58C-4CDB-B3C5-A9B93E6B9A7D@glasgow.ac.uk> Hi There, I was facing similar issues with Bio-Linux version of Tophat2 earlier this week. Tophat-reports was giving errors when the multi-threading parameter -p was specified by the user, and my version of BioLinux8 was running the latest version of Tophat2 (2.0.13). I fixed it by downloading the latest executables from Tophat2 website and it didn?t throw any errors with multi-threading. http://ccb.jhu.edu/software/tophat/index.shtml Sej On 26 Jan 2015, at 16:06, Suzanne Gomes > wrote: Hi! Brand new biolinux user here, and not really a computer person. My lab recently got a machine running biolinux 8 so we could do analysis with Galaxy. However I am having problems running Tophat and Tophat2. The first issue is with Tophat2, which gives the following error message: Fatal error: Tool execution failed Building a SMALL index [2015-01-19 12:10:58] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-01-19 12:10:58] Checking for Bowtie Bowtie 2 not found, checking for older version.. Bowtie version: 1.0.1.0 [2015-01-19 12:10:58] Checking for Samtools Samtools version: 0.1.19.0 [2015-01-19 12:10:58] Checking for Bowtie index files (genome).. Error: Could not find Bowtie index files (genome.*.ebwt) I read something in the mailing list from December that mentioned a problem with Tophat and bowtie not interacting properly, but it sounded as if that had been resolved. However, I think the install of biolinux on our computer was from before that fix (we had the install on a memory stick for a while before the computer was actually ready to go). But I am under the impression that biolinux automatically updates, so the fix should have been implemented after we installed, right? I?m not sure how to check if updates are installing. The second issue is with Tophat (which I tried after Tophat2 failed), which gives this error message: Error in tophat: tophat: option --no-closure-search not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html This error happens both with closure search turned on and turned off. Any suggestions for resolving these issues would be really appreciated. _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ian.Donaldson at manchester.ac.uk Wed Jan 28 06:22:16 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Wed, 28 Jan 2015 11:22:16 +0000 Subject: [Bio-Linux] Lack of UCSC tools in Bio-Linux 8 Message-ID: <7E756F18289AF64B967C333AC3BF7021017C46440D@MBXP02.ds.man.ac.uk> Hi, I have just stumbled across the fact that the UCSC tools are not installed = in Bio-Linux 8, apparently due to licensing issues. This means some tools = do not work in GALAXY. [galaxy-server-all] "This meta-package installs the full Galaxy environment including many thir= d party tools (see wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies). Exc= eptions are currently: LAJ - no source available UCSC tools - license restr= icts redistribution outside academia" What is the recommendation for installing this tools in to BL8, assuming ac= ademic usage? Thanks, Ian From tbooth at ceh.ac.uk Wed Jan 28 09:30:29 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 28 Jan 2015 14:30:29 +0000 Subject: [Bio-Linux] Lack of UCSC tools in Bio-Linux 8 In-Reply-To: <7E756F18289AF64B967C333AC3BF7021017C46440D@MBXP02.ds.man.ac.uk> References: <7E756F18289AF64B967C333AC3BF7021017C46440D@MBXP02.ds.man.ac.uk> Message-ID: <1422455429.14812.36.camel@wllt1771.nerc-wallingford.ac.uk> Hi Ian, We did make a Deb package, but we can't redistribute it as part of Bio-Linux: http://nebc.nerc.ac.uk/downloads/bio-linux/ucsc-tools-non-free_3.1-2_amd64.deb But in fact this is rather out of date, and installing the version from UCSC is just a matter of following their own instructions. As I recall it's very simple. So that would be the recommendation for installing the tools. Cheers, TIM On Wed, 2015-01-28 at 11:22 +0000, Ian Donaldson wrote: > Hi, > > I have just stumbled across the fact that the UCSC tools are not installed = > in Bio-Linux 8, apparently due to licensing issues. This means some tools = > do not work in GALAXY. > > [galaxy-server-all] > "This meta-package installs the full Galaxy environment including many thir= > d party tools (see wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies). Exc= > eptions are currently: LAJ - no source available UCSC tools - license restr= > icts redistribution outside academia" > > What is the recommendation for installing this tools in to BL8, assuming ac= > ademic usage? > > Thanks, > Ian > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From suzanneluziagomes at gmail.com Thu Jan 29 10:55:47 2015 From: suzanneluziagomes at gmail.com (Suzanne Gomes) Date: Thu, 29 Jan 2015 09:55:47 -0600 Subject: [Bio-Linux] Tophat2 multithread Message-ID: Hi, So I have Tophat2 running, but each run is taking at least 7 hours (not sure how long exactly as I?ve been leaving it overnight). Just wondering how I would go about increasing the number of threads Tophat2 uses in order to reduce the run time? Thanks Suzanne From gawbul at gmail.com Fri Jan 30 07:22:06 2015 From: gawbul at gmail.com (Steve Moss) Date: Fri, 30 Jan 2015 12:22:06 +0000 Subject: [Bio-Linux] Tophat2 multithread Message-ID: Dear Suzanne, Use the -p flag to tophat to increase the number of threads (see all flag options using tophat --help), e.g. tophat -p 24 for 24 threads. Note that not all stages of the pipeline are parallelised, however. Cheers, Steve On 30 January 2015 at 12:00, wrote: > Date: Thu, 29 Jan 2015 09:55:47 -0600 > From: Suzanne Gomes > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] Tophat2 multithread > Message-ID: > Content-Type: text/plain; charset=utf-8 > > Hi, > > So I have Tophat2 running, but each run is taking at least 7 hours (not > sure how long exactly as I?ve been leaving it overnight). Just wondering > how I would go about increasing the number of threads Tophat2 uses in order > to reduce the run time? > > Thanks > > Suzanne -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Ian.Donaldson at manchester.ac.uk Fri Jan 30 10:58:22 2015 From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson) Date: Fri, 30 Jan 2015 15:58:22 +0000 Subject: [Bio-Linux] missing sequences in Bio-Linux 8 GALAXY? Message-ID: <7E756F18289AF64B967C333AC3BF7021017C464646@MBXP02.ds.man.ac.uk> Hi, I am trying to use the 'fetch sequences > Extract Genomic DNA' tool in GALAXY. But I get a message saying that sequences are missing: "No sequences are available for 'mm9', request them by reporting this error." Can anyone give any guidance on how the sequence should be supplied? Also, I noticed the entire set of "operate on genomic intervals" tools are missing in Bio-Linux GALAXY. I personally consider them to be some of the most useful tools. I know how they can be added, but it would be nice/useful if they were already there :) Thanks, Ian -------------- next part -------------- An HTML attachment was scrubbed... URL: