From xmarti6 at xtec.cat Thu Feb 5 02:16:38 2015 From: xmarti6 at xtec.cat (=?UTF-8?Q?Xavier_Mart=C3=ADnez_Serrano?=) Date: Thu, 5 Feb 2015 08:16:38 +0100 Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster? Message-ID: Hi, We have 4 computers with ~20CPU each in a hospital research group and we would like to set a cluster with them. Which is the best suitable job scheduler for us if we are running Biolinux7 in three of them and Biolinux8 in the other? We have been looking at common job schedulers like: Slurm, SGE, Condor, Torque, ... but we wonder which best suits for our small resources, to make it as easy as possible. What can you recommend us? Many thanks in advance, Xavi -------------- next part -------------- An HTML attachment was scrubbed... URL: From xmarti6 at xtec.cat Thu Feb 5 02:23:08 2015 From: xmarti6 at xtec.cat (=?UTF-8?Q?Xavier_Mart=C3=ADnez_Serrano?=) Date: Thu, 5 Feb 2015 08:23:08 +0100 Subject: [Bio-Linux] Biolinux8 - Is there an installation for "server mode"? (without X11, just x2go connection) Message-ID: Hi, We are a research group working in metagenomics, and we would like to install Biolinux8 in a server recently acquired in "server mode", i.e. whithout X11 enabled, we just need a ssh connection and might be in some case an x2go connection. Is there an option to install Biolinux8 in such mode, revising the documentation online we could not see it. Many thanks, Xavi -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Thu Feb 5 05:31:22 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 5 Feb 2015 10:31:22 +0000 Subject: [Bio-Linux] Biolinux8 - Is there an installation for "server mode"? (without X11, just x2go connection) In-Reply-To: References: Message-ID: <54D3467A.8020903@abdn.ac.uk> On 05/02/15 07:23, Xavier Mart?nez Serrano wrote: > Hi, > > We are a research group working in metagenomics, and we would like to > install Biolinux8 in a server recently acquired in "server mode", i.e. > whithout X11 enabled, we just need a ssh connection and might be in > some case an x2go connection. > > Is there an option to install Biolinux8 in such mode, revising the > documentation online we could not see it. Hi, Xavi. We run Bio-Linux 8 on servers using Tim's default installation without any issues. If you want to use Bio-Linux as an "x2go" terminal server, you will need X11 and the MATE desktop installed anyway. The only real problem is you have to add the network configuration manually to prevent network manager from configuring the NIC's dynamically. You can use "network manager" to statically configure NIC's, but it is intended to be used to configure NIC's dynamically on laptops or workstations. 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 tony.travis at abdn.ac.uk Thu Feb 5 05:46:06 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 5 Feb 2015 10:46:06 +0000 Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster? In-Reply-To: References: Message-ID: <54D349EE.5050800@abdn.ac.uk> On 05/02/15 07:16, Xavier Mart?nez Serrano wrote: > Hi, > > We have 4 computers with ~20CPU each in a hospital research group and > we would like to set a cluster with them. Which is the best suitable job > scheduler for us if we are running Biolinux7 in three of them and > Biolinux8 in the other? > > We have been looking at common job schedulers like: Slurm, SGE, Condor, > Torque, ... but we wonder which best suits for our small resources, to > make it as easy as possible. > > What can you recommend us? Hi, Xavi. I've run SGE under Bio-Linux 7, but I would not advocate running a mixture of Bio-Linux 7 and 8. Tim's Bio-Linux 7-8 upgrade script works very well and I would recommend upgrading your Bio-Linux 7 machines to Bio-Linux 8. One thing you might consider looking at is Qlustar: https://qlustar.com/ They have made some commitment to support Debian/Med and I demo'ed a version with a Bio-Linux 'Front-end' at last year's Debian-Med Sprint: https://qlustar.com/news/qlustar-demo-debianmed-sprint Q-Leap gave a presentation at the recent Debian-Med Sprint, which I watched on Skype because I couldn't attend the meeting: https://wiki.debian.org/Sprints/2015/DebianMed2015 Maybe Tim can tell you more because he was there. It's pay-for software, and I have some reservations about their licensing model, but from what I've seen of it Qlustar is very good cluster software. Q-Leap support Slurm in particular, but do consider Amdahl's Law: http://en.wikipedia.org/wiki/Amdahl's_law I'm working with Luca Clivio to install a Qlustar cluster with a Bio-Linux Front-end at MNI (Mario Negri Institute) in Milan: http://www.marionegri.it/mn/it/index.html Please contact Luca directly if you are interested in this project. 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 tbooth at ceh.ac.uk Thu Feb 5 06:02:12 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 5 Feb 2015 11:02:12 +0000 Subject: [Bio-Linux] Biolinux8 - Is there an installation for "server mode"? (without X11, just x2go connection) In-Reply-To: <54D3467A.8020903@abdn.ac.uk> References: <54D3467A.8020903@abdn.ac.uk> Message-ID: <1423134132.23727.117.camel@wllt1771.nerc-wallingford.ac.uk> Hi, Tony's right - the Bio-Linux ISO is based on the Ubuntu desktop ISO, so you basically need an X-session to run the installer even if you subsequently remove X and run the thing headless. It's possible to strip out the X server packages while still retaining the libraries needed by MATE for x2go but for simplicity I'd just take out LightDM so X is present but never started. By "add the network configuration manually" this means that if you set your settings for any network card in /etc/network/interfaces then when the NM daemon is restarted it will leave that card alone. In my experience NM now works very well but on a server with fixed network routing it's just another layer of complexity you don't need. Use the command "nmcli d" to see what devices NM thinks it is managing. Cheers, TIM On Thu, 2015-02-05 at 10:31 +0000, Tony Travis wrote: > On 05/02/15 07:23, Xavier Mart?nez Serrano wrote: > > Hi, > > > > We are a research group working in metagenomics, and we would like to > > install Biolinux8 in a server recently acquired in "server mode", i.e. > > whithout X11 enabled, we just need a ssh connection and might be in > > some case an x2go connection. > > > > Is there an option to install Biolinux8 in such mode, revising the > > documentation online we could not see it. > > Hi, Xavi. > > We run Bio-Linux 8 on servers using Tim's default installation without > any issues. If you want to use Bio-Linux as an "x2go" terminal server, > you will need X11 and the MATE desktop installed anyway. The only real > problem is you have to add the network configuration manually to prevent > network manager from configuring the NIC's dynamically. You can use > "network manager" to statically configure NIC's, but it is intended to > be used to configure NIC's dynamically on laptops or workstations. > > 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 -- 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 tbooth at ceh.ac.uk Thu Feb 5 06:18:22 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 5 Feb 2015 11:18:22 +0000 Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster? In-Reply-To: References: Message-ID: <1423135102.23727.126.camel@wllt1771.nerc-wallingford.ac.uk> Hi Xavi, To be honest I don't really know. Hopefully someone on the list will have some practical experience to share. We use Torqe on a cluster here at CEH but it's not actually running Bio-Linux and I had no part in setting it up so I don't know how easy it is to configure. I have experience with Condor and I don't think it is what you need at all. SGE used to be good but Oracle have not looked after it well. My guess would be that Slurm is the best answer for you. The latest version of QIIME recommends it, which is a good sign, and I'm told that set-up for a small cluster is "very simple". You might well have issues with running a cluster of Bio-Linux 7 and 8 machines, though, because the packaged versions of Slurm and of the bioinformatics software will be different on the different nodes. I'd strongly recommend upgrading everything to the same version. Also, you really should set up a fast shared NFS drive that all the machines can see. Running a cluster without a shared filesystem is possible but for most bioinformatics tasks it's highly impractical. Cheers, TIM On Thu, 2015-02-05 at 07:16 +0000, Xavier Mart?nez Serrano wrote: > Hi, > > We have 4 computers with ~20CPU each in a hospital research group and > we would like to set a cluster with them. Which is the best suitable > job scheduler for us if we are running Biolinux7 in three of them and > Biolinux8 in the other? > > We have been looking at common job schedulers like: Slurm, SGE, > Condor, Torque, ... but we wonder which best suits for our small > resources, to make it as easy as possible. > > What can you recommend us? > > Many thanks in advance, > Xavi > -- 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 tbooth at ceh.ac.uk Thu Feb 5 08:16:22 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 5 Feb 2015 13:16:22 +0000 Subject: [Bio-Linux] qiime V. 1.9.0 on BioLinux? In-Reply-To: References: <344AE70EFD3E8C40BB1ADFE7F415813B01D458E301C3@Geuspost01.geus.dk> Message-ID: <1423142182.23727.131.camel@wllt1771.nerc-wallingford.ac.uk> Hi, Several people are asking about QIIME 1.9 on Bio-Linux. I was hoping to have a package ready this week but it turns out to be a bigger job than I anticipated, plus I've also had other projects putting demands on my time. Therefore it's going to be a little while. I'm hoping to get it done next week but I can't promise anything before the end of the month. 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 xmarti6 at xtec.cat Thu Feb 5 09:19:58 2015 From: xmarti6 at xtec.cat (=?UTF-8?Q?Xavier_Mart=C3=ADnez_Serrano?=) Date: Thu, 5 Feb 2015 15:19:58 +0100 Subject: [Bio-Linux] Bio-Linux Digest, Vol 77, Issue 2 In-Reply-To: References: Message-ID: Thank you very much to all for all your sharings, they will be really useful to us to set everything up. Following your extended comments seems that the best option will probably be to use Slurm and Uprade all Biolinux to v8, and installing MATE on top. The network will be configured manually. We will probably do all this next week. I'll let you know if we get into big issues; hopefully not! :) Best, greetings, Xavi 2015-02-05 12:18 GMT+01:00 : > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-Linux digest..." > > > Today's Topics: > > 1. Biolinux8 - Best job scheduler for small cluster? > (Xavier Mart?nez Serrano) > 2. Biolinux8 - Is there an installation for "server mode"? > (without X11, just x2go connection) (Xavier Mart?nez Serrano) > 3. Re: Biolinux8 - Is there an installation for "server mode"? > (without X11, just x2go connection) (Tony Travis) > 4. Re: Biolinux8 - Best job scheduler for small cluster? > (Tony Travis) > 5. Re: Biolinux8 - Is there an installation for "server mode"? > (without X11, just x2go connection) (Tim Booth) > 6. Re: Biolinux8 - Best job scheduler for small cluster? (Tim Booth) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 5 Feb 2015 08:16:38 +0100 > From: Xavier Mart?nez Serrano > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster? > Message-ID: > < > CAPYyywinF97V3eiL_CfZEDE5uS9i_Z0o89d3x_9y_cf4QZ54Xw at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > We have 4 computers with ~20CPU each in a hospital research group and we > would like to set a cluster with them. Which is the best suitable job > scheduler for us if we are running Biolinux7 in three of them and Biolinux8 > in the other? > > We have been looking at common job schedulers like: Slurm, SGE, Condor, > Torque, ... but we wonder which best suits for our small resources, to make > it as easy as possible. > > What can you recommend us? > > Many thanks in advance, > Xavi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150205/048bb640/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Thu, 5 Feb 2015 08:23:08 +0100 > From: Xavier Mart?nez Serrano > To: bio-linux at nebclists.nerc.ac.uk > Subject: [Bio-Linux] Biolinux8 - Is there an installation for "server > mode"? (without X11, just x2go connection) > Message-ID: > < > CAPYyywjGoQ9orbWs5WQq2GJpYvesFY3Adde0z8wRhaWWr+vgzg at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > We are a research group working in metagenomics, and we would like to > install Biolinux8 in a server recently acquired in "server mode", i.e. > whithout X11 enabled, we just need a ssh connection and might be in some > case an x2go connection. > > Is there an option to install Biolinux8 in such mode, revising the > documentation online we could not see it. > > Many thanks, > Xavi > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150205/8ef9f33e/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Thu, 5 Feb 2015 10:31:22 +0000 > From: Tony Travis > To: > Subject: Re: [Bio-Linux] Biolinux8 - Is there an installation for > "server mode"? (without X11, just x2go connection) > Message-ID: <54D3467A.8020903 at abdn.ac.uk> > Content-Type: text/plain; charset="windows-1252" > > On 05/02/15 07:23, Xavier Mart?nez Serrano wrote: > > Hi, > > > > We are a research group working in metagenomics, and we would like to > > install Biolinux8 in a server recently acquired in "server mode", i.e. > > whithout X11 enabled, we just need a ssh connection and might be in > > some case an x2go connection. > > > > Is there an option to install Biolinux8 in such mode, revising the > > documentation online we could not see it. > > Hi, Xavi. > > We run Bio-Linux 8 on servers using Tim's default installation without > any issues. If you want to use Bio-Linux as an "x2go" terminal server, > you will need X11 and the MATE desktop installed anyway. The only real > problem is you have to add the network configuration manually to prevent > network manager from configuring the NIC's dynamically. You can use > "network manager" to statically configure NIC's, but it is intended to > be used to configure NIC's dynamically on laptops or workstations. > > 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. > > > ------------------------------ > > Message: 4 > Date: Thu, 5 Feb 2015 10:46:06 +0000 > From: Tony Travis > To: > Cc: Luca Clivio > Subject: Re: [Bio-Linux] Biolinux8 - Best job scheduler for small > cluster? > Message-ID: <54D349EE.5050800 at abdn.ac.uk> > Content-Type: text/plain; charset="windows-1252" > > On 05/02/15 07:16, Xavier Mart?nez Serrano wrote: > > Hi, > > > > We have 4 computers with ~20CPU each in a hospital research group and > > we would like to set a cluster with them. Which is the best suitable job > > scheduler for us if we are running Biolinux7 in three of them and > > Biolinux8 in the other? > > > > We have been looking at common job schedulers like: Slurm, SGE, Condor, > > Torque, ... but we wonder which best suits for our small resources, to > > make it as easy as possible. > > > > What can you recommend us? > > Hi, Xavi. > > I've run SGE under Bio-Linux 7, but I would not advocate running a > mixture of Bio-Linux 7 and 8. Tim's Bio-Linux 7-8 upgrade script works > very well and I would recommend upgrading your Bio-Linux 7 machines to > Bio-Linux 8. One thing you might consider looking at is Qlustar: > > https://qlustar.com/ > > They have made some commitment to support Debian/Med and I demo'ed a > version with a Bio-Linux 'Front-end' at last year's Debian-Med Sprint: > > https://qlustar.com/news/qlustar-demo-debianmed-sprint > > Q-Leap gave a presentation at the recent Debian-Med Sprint, which I > watched on Skype because I couldn't attend the meeting: > > https://wiki.debian.org/Sprints/2015/DebianMed2015 > > Maybe Tim can tell you more because he was there. It's pay-for software, > and I have some reservations about their licensing model, but from what > I've seen of it Qlustar is very good cluster software. Q-Leap support > Slurm in particular, but do consider Amdahl's Law: > > http://en.wikipedia.org/wiki/Amdahl's_law > > I'm working with Luca Clivio to install a Qlustar cluster with a > Bio-Linux Front-end at MNI (Mario Negri Institute) in Milan: > > http://www.marionegri.it/mn/it/index.html > > Please contact Luca directly if you are interested in this project. > > 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. > > > ------------------------------ > > Message: 5 > Date: Thu, 5 Feb 2015 11:02:12 +0000 > From: Tim Booth > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] Biolinux8 - Is there an installation for > "server mode"? (without X11, just x2go connection) > Message-ID: > <1423134132.23727.117.camel at wllt1771.nerc-wallingford.ac.uk> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > Tony's right - the Bio-Linux ISO is based on the Ubuntu desktop ISO, so > you basically need an X-session to run the installer even if you > subsequently remove X and run the thing headless. It's possible to > strip out the X server packages while still retaining the libraries > needed by MATE for x2go but for simplicity I'd just take out LightDM so > X is present but never started. > > By "add the network configuration manually" this means that if you set > your settings for any network card in /etc/network/interfaces then when > the NM daemon is restarted it will leave that card alone. In my > experience NM now works very well but on a server with fixed network > routing it's just another layer of complexity you don't need. Use the > command "nmcli d" to see what devices NM thinks it is managing. > > Cheers, > > TIM > > On Thu, 2015-02-05 at 10:31 +0000, Tony Travis wrote: > > On 05/02/15 07:23, Xavier Mart?nez Serrano wrote: > > > Hi, > > > > > > We are a research group working in metagenomics, and we would like to > > > install Biolinux8 in a server recently acquired in "server mode", i.e. > > > whithout X11 enabled, we just need a ssh connection and might be in > > > some case an x2go connection. > > > > > > Is there an option to install Biolinux8 in such mode, revising the > > > documentation online we could not see it. > > > > Hi, Xavi. > > > > We run Bio-Linux 8 on servers using Tim's default installation without > > any issues. If you want to use Bio-Linux as an "x2go" terminal server, > > you will need X11 and the MATE desktop installed anyway. The only real > > problem is you have to add the network configuration manually to prevent > > network manager from configuring the NIC's dynamically. You can use > > "network manager" to statically configure NIC's, but it is intended to > > be used to configure NIC's dynamically on laptops or workstations. > > > > 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 > > -- > 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 > > > > ------------------------------ > > Message: 6 > Date: Thu, 5 Feb 2015 11:18:22 +0000 > From: Tim Booth > To: Bio-Linux help and discussion > Cc: Xavier Mart?nez Serrano > Subject: Re: [Bio-Linux] Biolinux8 - Best job scheduler for small > cluster? > Message-ID: > <1423135102.23727.126.camel at wllt1771.nerc-wallingford.ac.uk> > Content-Type: text/plain; charset="UTF-8" > > Hi Xavi, > > To be honest I don't really know. Hopefully someone on the list will > have some practical experience to share. We use Torqe on a cluster here > at CEH but it's not actually running Bio-Linux and I had no part in > setting it up so I don't know how easy it is to configure. > > I have experience with Condor and I don't think it is what you need at > all. SGE used to be good but Oracle have not looked after it well. > > My guess would be that Slurm is the best answer for you. The latest > version of QIIME recommends it, which is a good sign, and I'm told that > set-up for a small cluster is "very simple". You might well have issues > with running a cluster of Bio-Linux 7 and 8 machines, though, because > the packaged versions of Slurm and of the bioinformatics software will > be different on the different nodes. I'd strongly recommend upgrading > everything to the same version. > > Also, you really should set up a fast shared NFS drive that all the > machines can see. Running a cluster without a shared filesystem is > possible but for most bioinformatics tasks it's highly impractical. > > Cheers, > > TIM > > > > > On Thu, 2015-02-05 at 07:16 +0000, Xavier Mart?nez Serrano wrote: > > Hi, > > > > We have 4 computers with ~20CPU each in a hospital research group and > > we would like to set a cluster with them. Which is the best suitable > > job scheduler for us if we are running Biolinux7 in three of them and > > Biolinux8 in the other? > > > > We have been looking at common job schedulers like: Slurm, SGE, > > Condor, Torque, ... but we wonder which best suits for our small > > resources, to make it as easy as possible. > > > > What can you recommend us? > > > > Many thanks in advance, > > Xavi > > > > -- > 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 > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > ------------------------------ > > End of Bio-Linux Digest, Vol 77, Issue 2 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Thu Feb 5 09:36:44 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 5 Feb 2015 14:36:44 +0000 Subject: [Bio-Linux] Bio-Linux Digest, Vol 77, Issue 2 In-Reply-To: References: Message-ID: <54D37FFC.1070600@abdn.ac.uk> On 05/02/15 14:19, Xavier Mart?nez Serrano wrote: > Thank you very much to all for all your sharings, they will be really > useful to us to set everything up. > > Following your extended comments seems that the best option will > probably be to use Slurm and Uprade > all Biolinux to v8, and installing MATE on top. The network will be > configured manually. We will probably do > all this next week. I'll let you know if we get into big issues; > hopefully not! :) Hi, Xavi. One thing to note is that you might have problems with Qt if you run "RStudio" on a remote MATE desktop. Tim has suggested a work-around for this problem that I've used to run RStudio on "x2go" terminal servers: > cd /usr/lib/rstudio/bin > mkdir notused > mv -i libQ* notused/ > mv -i qt.conf notused/ It seems that the Qt libraries bundled with RStudio can cause problems. In our case, all the necessary Qt libraries were already installed: > libqt4-network > libqt4-opengl > libqt4-svg > libqt4-xml > libqt4-xmlpatterns > libqtcore4 > libqtdbus4 > libqtgui4 > libqtwebkit4 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 jmategkox2 at gmail.com Thu Feb 5 11:21:49 2015 From: jmategkox2 at gmail.com (James Mategko) Date: Thu, 5 Feb 2015 08:21:49 -0800 Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster? In-Reply-To: <1423135102.23727.126.camel@wllt1771.nerc-wallingford.ac.uk> References: <1423135102.23727.126.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: Hi Xavier, If you are running metagenomics with Qiime version 1.9 adds a new script called "start parallel jobs with slurm". I'm not familiar with its inner workings since I'm still using the default Qiime 1.8 in Bio-linux 8, but it looks promising. http://qiime.org/scripts/start_parallel_jobs_slurm.html Best Regards, - James On Thu, Feb 5, 2015 at 3:18 AM, Tim Booth wrote: > Hi Xavi, > > To be honest I don't really know. Hopefully someone on the list will > have some practical experience to share. We use Torqe on a cluster here > at CEH but it's not actually running Bio-Linux and I had no part in > setting it up so I don't know how easy it is to configure. > > I have experience with Condor and I don't think it is what you need at > all. SGE used to be good but Oracle have not looked after it well. > > My guess would be that Slurm is the best answer for you. The latest > version of QIIME recommends it, which is a good sign, and I'm told that > set-up for a small cluster is "very simple". You might well have issues > with running a cluster of Bio-Linux 7 and 8 machines, though, because > the packaged versions of Slurm and of the bioinformatics software will > be different on the different nodes. I'd strongly recommend upgrading > everything to the same version. > > Also, you really should set up a fast shared NFS drive that all the > machines can see. Running a cluster without a shared filesystem is > possible but for most bioinformatics tasks it's highly impractical. > > Cheers, > > TIM > > > > > On Thu, 2015-02-05 at 07:16 +0000, Xavier Mart?nez Serrano wrote: > > Hi, > > > > We have 4 computers with ~20CPU each in a hospital research group and > > we would like to set a cluster with them. Which is the best suitable > > job scheduler for us if we are running Biolinux7 in three of them and > > Biolinux8 in the other? > > > > We have been looking at common job schedulers like: Slurm, SGE, > > Condor, Torque, ... but we wonder which best suits for our small > > resources, to make it as easy as possible. > > > > What can you recommend us? > > > > Many thanks in advance, > > Xavi > > > > -- > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Simon.Wagstaff at lstmed.ac.uk Fri Feb 6 14:38:56 2015 From: Simon.Wagstaff at lstmed.ac.uk (Simon Wagstaff) Date: Fri, 6 Feb 2015 19:38:56 +0000 Subject: [Bio-Linux] Stacks RAD-seq software on Bio-Linux In-Reply-To: <1422023999.13659.52.camel@wllt1771.nerc-wallingford.ac.uk> References: <1422023999.13659.52.camel@wllt1771.nerc-wallingford.ac.uk> Message-ID: <3ED46ED7-9B83-43C0-8C7A-1D2D5D578329@lstmed.ac.uk> Hi Tim, Thanks again for doing this. I?ve installed stacks web but got some errors (below) when attempting to create the database. I?m not familiar with how it works so not sure if this is a problem? Thanks, Simon simonw at PowerEdge-R820[simonw] sudo stacks-setup-database gweedall [ 7:26PM] ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' (using password: YES) Making database gweedall_radtags for gweedall ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' (using password: YES) Aborting. simonw at PowerEdge-R820[simonw] [ 7:27PM] _________________________________ Simon Wagstaff Tel: +44-(0)151-705-3164 Fax: +44-(0)151-705-3371 email: simon.wagstaff at lstmed.ac.uk On 23 Jan 2015, at 14:39, Tim Booth > wrote: 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 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux ________________________________ [http://www.lstmed.ac.uk/images/lstm_email_logo.gif] This e-mail message is sent on behalf of the Liverpool School of Tropical Medicine, a charitable company limited by guarantee registered in England and Wales with company number 222655 and whose registered office is at Pembroke Place Liverpool L3 5QA ("LSTM") The contents of this e-mail are subject to LSTM?s email disclaimer found at: http://www.lstmed.ac.uk/disclaimer/email-disclaimer -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Sun Feb 8 05:11:49 2015 From: gawbul at gmail.com (Steve Moss) Date: Sun, 8 Feb 2015 10:11:49 +0000 Subject: [Bio-Linux] Stacks RAD-seq software on Bio-Linux Message-ID: Dear Simon, It seems as though it can't authenticate with your database. See this link http://creskolab.uoregon.edu/stacks/manual/#install specifically "Section 2.3 Edit the MySQL configuration file" that details setting up MySQL users. Use mysql -u root to login to the MySQL shell and add new users. You should then edit /usr/local/share/stacks/sql/mysql.cnf to include the appropriate user and password for connection. It's not a good idea to use root for stacks to connect, so you should create an additional stacks user in MySQL. Cheers, Steve Message: 1 > Date: Fri, 6 Feb 2015 19:38:56 +0000 > From: Simon Wagstaff > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] Stacks RAD-seq software on Bio-Linux > Message-ID: <3ED46ED7-9B83-43C0-8C7A-1D2D5D578329 at lstmed.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Hi Tim, > Thanks again for doing this. I?ve installed stacks web but got some errors > (below) when attempting to create the database. I?m not familiar with how > it works so not sure if this is a problem? > > Thanks, > > Simon > > > simonw at PowerEdge-R820[simonw] sudo stacks-setup-database gweedall [ > 7:26PM] > ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' > (using password: YES) > Making database gweedall_radtags for gweedall > ERROR 1045 (28000): Access denied for user 'debian-sys-maint'@'localhost' > (using password: YES) > Aborting. > simonw at PowerEdge-R820[simonw] [ > 7:27PM] > > > _________________________________ > > Simon Wagstaff > Tel: +44-(0)151-705-3164 > Fax: +44-(0)151-705-3371 > email: simon.wagstaff at lstmed.ac.uk > -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Mon Feb 9 06:48:04 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 9 Feb 2015 11:48:04 +0000 Subject: [Bio-Linux] Fwd: daphnia-genomics Environmental Genomics Course: Birmingham March 23-27 Message-ID: <1423482484.13065.11.camel@wllt1771.nerc-wallingford.ac.uk> Dear All, Apologies if you receive this multiple times, but I hope this will be of interest to some people on this list. For any queries please respond directly to John rather than to me or to the mailing list. Cheers, TIM --- From: John Colbourne > Subject: daphnia-genomics Environmental Genomics Course: Birmingham March 23-27 > Date: 8 February 2015 06:49:32 GMT > To: "daphnia-genomics at lists.bham.ac.uk" > > NERC-MDIBL Environmental Genomics Course, 2015 > Online Registration Site: www.birmingham.ac.uk/EnGen > Dates: March 23-27, 2015 > Location: University of Birmingham, UK > Number of Places: Between 25 and 50 > Open to: Participation is open to everyone. > Priority is given to NERC-funded PhD students and early-career postdocs. Confirmation to attend will be announced March 2, 2015. > Course Leaders: John Colbourne, Joseph Shaw, Mark Viant, Xin Zhou > Research Organizations Involved: University of Birmingham (UK), BGI China National GeneBank (Shenzhen, China), Mount Desert Island Biological Laboratory (USA) > > Description This training opportunity in Environmental Genomics is the second European/UK instalment of a successful annual course originating from Mount Desert Island Biological Laboratory. It trains PhD students and early career postdoctoral scientists to investigate how gene function is influenced by environmental conditions while accounting for variation that exists within and among natural populations. The course is built on the paradigm that the multidisciplinary research field encompassing ecology, evolution, toxicology, biostatistics and informatics will most effectively grow by training early career environmental scientists to properly design comprehensive, large-scale, experiments enabled by drastically increased sample-throughput and lower costs. Most importantly, the challenges of manipulating and analysing population-level genomics (big) data must be addressed. > The course provides intensive training in seminar and laboratory formats, especially around expression profiling by RNA-Seq. Topics covered include bioinformatics using sequence analysis workflows and R statistical analysis tools, plus experimental design for environmental genomics research. For the laboratory, participants will be introduced to automated sample preparation as well as preparing their own RNA-sequencing libraries. The course provides a significant introduction and some hands-on training experience so that participants can initiate their own environmental genomics study and network with others in the field to launch Environmental Scientist careers in academia and industry. > Course Content Participants are taught using open-source analysis tools and existing OMICS data. > Course Presentations ? Library construction methods and QC ? Introduction to automation systems ? Introduction to the sequence data workflow ? Software solutions for the sequence and metabolomics data workflows & their applications for environmental research ? Review of sequencing technology, its strengths and weaknesses ? RNA-Seq alignment to individualize transcriptomes ? Statistical considerations for analysing genome-scale data > Bioinformatics Training ? Introduction to R ? Visualization of sequence and metabolomics data for quality assurance ? Visualization of complex data ? Navigating the command line ? Data analysis workshop using R to analyse Tuxedo output ? Gene set enrichment analysis ? Exploring genome sequence variation ? Help desk to explore participants research questions > Synthesis Sessions ? Models in search of ecology vs ecology in search of models ? What can I extract from the sequence data for my investigations ? Integrating omics data ? How do I obtain funding for my Environmental Genomics project > Evening Lecture Series There will be four evening lectures designed to highlight environmental omic applications that draw on the expertise of our guest faculty. > Daphnia is used for training because of their growing use as model systems for environmental genomics and for improving environmental health protection, yet the skills learned during the course will be applicable to all study systems with mature genomics resources. > > School of Biosciences, The University of Birmingham Birmingham, B15 2TT, United Kingdom > Mount Desert Island Biological Laboratory Old Bar Harbor Rd., Salisbury Cove, ME 04672 From tbooth at ceh.ac.uk Mon Feb 9 07:39:00 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 9 Feb 2015 12:39:00 +0000 Subject: [Bio-Linux] Stacks RAD-seq software on Bio-Linux In-Reply-To: References: Message-ID: <1423485540.13065.31.camel@wllt1771.nerc-wallingford.ac.uk> Hi Simon, Please do not try to fix the database by following manual setup instructions in the upstream documentation. The entire point of this packaging exercise was to avoid manual and potentially insecure configuration of MySQL! I got a long reply from the Stacks author regarding my approach to the packaging. He pointed out that my default assumption of naming the database after the user was wrong - the database should always be named after the experiment - which I can easily do (and you can do so now using the -d flag in any case). Apart from that he pointed out a couple of minor issues I will go ahead and change but the database security settings will stay as they are in the current package. The actual error you have relates to the debian-sys-maint account which is a standard part of the Debian MySQL installation and allows the Deb system scripts to configure the database. If this account isn't logging in then there is a problem with your MySQL installation. Please try reinitialising it like so: $ sudo mv /etc/mysql/debian.cnf /etc/mysql/debian.cnf.bak $ sudo dpkg-reconfigure -plow mysql-server-5.5 Does that help? Cheers, TIM On Sun, 2015-02-08 at 10:11 +0000, Steve Moss wrote: > Dear Simon, > > > It seems as though it can't authenticate with your database. See this > link http://creskolab.uoregon.edu/stacks/manual/#install specifically > "Section 2.3 Edit the MySQL configuration file" that details setting > up MySQL users. Use mysql -u root to login to the MySQL shell and add > new users. You should then edit /usr/local/share/stacks/sql/mysql.cnf > to include the appropriate user and password for connection. It's not > a good idea to use root for stacks to connect, so you should create an > additional stacks user in MySQL. > > Cheers, > > Steve > > Message: 1 > Date: Fri, 6 Feb 2015 19:38:56 +0000 > From: Simon Wagstaff > To: Bio-Linux help and discussion > > Subject: Re: [Bio-Linux] Stacks RAD-seq software on Bio-Linux > Message-ID: > <3ED46ED7-9B83-43C0-8C7A-1D2D5D578329 at lstmed.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Hi Tim, > Thanks again for doing this. I?ve installed stacks web but got > some errors (below) when attempting to create the database. > I?m not familiar with how it works so not sure if this is a > problem? > > Thanks, > > Simon > > > simonw at PowerEdge-R820[simonw] sudo stacks-setup-database > gweedall [ 7:26PM] > ERROR 1045 (28000): Access denied for user > 'debian-sys-maint'@'localhost' (using password: YES) > Making database gweedall_radtags for gweedall > ERROR 1045 (28000): Access denied for user > 'debian-sys-maint'@'localhost' (using password: YES) > Aborting. > simonw at PowerEdge-R820[simonw] > [ 7:27PM] > > > _________________________________ > > Simon Wagstaff > Tel: +44-(0)151-705-3164 > Fax: +44-(0)151-705-3371 > email: > simon.wagstaff at lstmed.ac.uk > > > > -- > > Steve Moss > about.me/gawbul > Steve Moss on about.me > -- 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 Fri Feb 13 15:38:11 2015 From: suzanneluziagomes at gmail.com (Suzanne Gomes) Date: Fri, 13 Feb 2015 14:38:11 -0600 Subject: [Bio-Linux] Boiling updates In-Reply-To: References: Message-ID: <27EEB58C-CC1F-4C93-843A-2FF479978917@gmail.com> Hi, I updated biolinux today from the software updater, and restarted the computer. Now, it?s allowing me to login, but once I log in there are no icons on the screen, nothing. Just the wallpaper. Any idea what is going on??? Is there something wrong with this update? Suzanne From tbooth at ceh.ac.uk Mon Feb 16 05:57:04 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 16 Feb 2015 10:57:04 +0000 Subject: [Bio-Linux] Boiling updates In-Reply-To: <27EEB58C-CC1F-4C93-843A-2FF479978917@gmail.com> References: <27EEB58C-CC1F-4C93-843A-2FF479978917@gmail.com> Message-ID: <1424084224.4098.45.camel@wllt1771.nerc-wallingford.ac.uk> Hi Suzanne, Sorry to hear that. I'm not aware of any problems with updates (boiling or otherwise) this week, but I've seen similar problems before - most recently this issue which affected VM users: http://nebclists.nerc.ac.uk/pipermail/bio-linux/2015-January/000742.html It's normally due to a graphics driver update issue. I'm assuming you are not using Bio-Linux in a VM here? Do you use the NVidia 3rd party driver packages? If not: 1) At the login screen select the MATE desktop 2) Open a new terminal and type the following (each on one line) 3) sudo apt-get purge nvidia-331-updates nvidia-opencl-icd-331-updates nvidia-prime nvidia-settings libhwloc-plugins 4) sudo apt-get update 5) sudo apt-get dist-upgrade 6) mkdir my_old_dot_files 7) mv ~/.local ~/.g* my_old_dot_files/ 8) sudo reboot Does that solve it? If not, please describe what happens as you try to follow the above steps and hopefully that will give me a clue what is wrong. Cheers, TIM On Fri, 2015-02-13 at 20:38 +0000, Suzanne Gomes wrote: > Hi, > > I updated biolinux today from the software updater, and restarted the > computer. Now, it?s allowing me to login, but once I log in there are > no icons on the screen, nothing. Just the wallpaper. Any idea what is > going on??? Is there something wrong with this update? > > Suzanne > _______________________________________________ > 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 g.zancolli at bangor.ac.uk Mon Feb 16 06:38:17 2015 From: g.zancolli at bangor.ac.uk (Giulia Zancolli) Date: Mon, 16 Feb 2015 11:38:17 +0000 Subject: [Bio-Linux] assigning bash variables Message-ID: Hello, I'm using Biolinux 8 on a university PC (I login as user and not admin) and I'm having problem with a very basic task - assigning variables in the shell! I type something very simple like a=1 and I get the error: command "a=" not found or the following (which was working perfectly in Linux on my laptop) LIST="$(ls | grep "fastq$")" And I get the error "Illegal variable name" What might be wrong? Any clue is very appreciated! Giulia Dr Giulia Zancolli Molecular Ecology and Fisheries Genetics Lab School of Biological Sciences Bangor University Environment Centre Wales Bangor LL57 2UW UK Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bt27uk at yahoo.no Mon Feb 16 09:36:40 2015 From: bt27uk at yahoo.no (Bela Tiwari) Date: Mon, 16 Feb 2015 14:36:40 +0000 (UTC) Subject: [Bio-Linux] assigning bash variables In-Reply-To: References: Message-ID: <173629059.7694640.1424097400479.JavaMail.yahoo@mail.yahoo.com> Hello, >I?m using Biolinux 8 on a university PC (I login as user and not admin) and I?m having problem with >a very basic task ? assigning variables in the shell! If you're trying to set environmental variables, you'll need to use export before the rest of the statement. e.g. export MYVAR=1 Setting environmental variables is covered on page 29 of the Bio-Linux tutorial: http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf I hope that's the information you were looking for. Best wishes, Bela Den Mandag, 16. februar 2015 12.38 skrev Giulia Zancolli : Hello, I?m using Biolinux 8 on a university PC (I login as user and not admin) and I?m having problem with a very basic task ? assigning variables in the shell! ? I type something very simple like ? a=1 ? and I get the error: command ?a=? not found or the following (which was working perfectly in Linux on my laptop) ? LIST="$(ls | grep "fastq$")" ? And I get the error ?Illegal variable name? ? What might be wrong? ? Any clue is very appreciated! ? Giulia ? Dr Giulia Zancolli Molecular Ecology and Fisheries Genetics Lab School of Biological Sciences???? Bangor University Environment Centre Wales Bangor LL57 2UW????????????????? UK? ? ? | Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor.This email and any attachments may contain confidential material and is solely for the use of the intended recipient(s). If you have received this email in error, please notify the sender immediately and delete this email. If you are not the intended recipient(s), you must not use, retain or disclose any information contained in this email. Any views or opinions are solely those of the sender and do not necessarily represent those of Bangor University. Bangor University does not guarantee that this email or any attachments are free from viruses or 100% secure. Unless expressly stated in the body of the text of the email, this email is not intended to form a binding contract - a list of authorised signatories is available from the Bangor University Finance Office. | _______________________________________________ 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 Feb 16 10:24:11 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 16 Feb 2015 15:24:11 +0000 Subject: [Bio-Linux] assigning bash variables In-Reply-To: <173629059.7694640.1424097400479.JavaMail.yahoo@mail.yahoo.com> References: <173629059.7694640.1424097400479.JavaMail.yahoo@mail.yahoo.com> Message-ID: <1424100251.12415.15.camel@wllt1771.nerc-wallingford.ac.uk> Hi Giulia, Someone has switched your login shell to TCSH (or maybe CSH). I've confirmed that when I run those commands under TCSH I get the same errors as you. You can set your shell preference back by using the 'chsh' command. You'll be prompted for the shell to use and you can either go for /bin/zsh or /bin/bash. ZSH is the Bio-Linux default as I find it a more friendly interactive shell when using tab-completion etc. but BASH is the more usual Linux shell and the default for Ubuntu. Both are supported on BL and both will accept variable assignments the way you are trying (and as Bela noted, both use "export" to turn shell variables into environment variables). Log out then in again to get the new shell. If for some reason you don't want to run "chsh" on the account just run "exec zsh" and you'll be in ZSH until you close the terminal. Cheers, TIM On Mon, 2015-02-16 at 14:36 +0000, Bela Tiwari wrote: > Hello, > > > > >I?m using Biolinux 8 on a university PC (I login as user and not > admin) and I?m having problem with > >a very basic task ? assigning variables in the shell! > > > If you're trying to set environmental variables, you'll need to use > export before the rest of the statement. > > e.g. > > > export MYVAR=1 > > > Setting environmental variables is covered on page 29 of the Bio-Linux > tutorial: > > > > http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl8_latest.pdf > > > > I hope that's the information you were looking for. > > > > Best wishes, > > > > Bela > > > > Den Mandag, 16. februar 2015 12.38 skrev Giulia Zancolli > : > > > > Hello, > I?m using Biolinux 8 on a university PC (I login as user and not > admin) and I?m having problem with a very basic task ? assigning > variables in the shell! > > I type something very simple like > > a=1 > > and I get the error: command ?a=? not found > > or the following (which was working perfectly in Linux on my laptop) > > LIST="$(ls | grep "fastq$")" > > And I get the error ?Illegal variable name? > > What might be wrong? > > Any clue is very appreciated! > > Giulia > > Dr Giulia Zancolli > Molecular Ecology and Fisheries Genetics Lab > School of Biological Sciences > Bangor University > Environment Centre Wales > Bangor LL57 2UW > UK > > > Rhif Elusen Gofrestredig 1141565 - Registered Charity No. 1141565 > Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi, > gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig > gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y > neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar unwaith > a dilewch y neges. Os na fwriadwyd anfon y neges atoch chi, rhaid i > chi beidio a defnyddio, cadw neu ddatgelu unrhyw wybodaeth a gynhwysir > ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i hanfonodd yn > unig ac nid yw o anghenraid yn cynrychioli barn Prifysgol Bangor. Nid > yw Prifysgol Bangor yn gwarantu bod y neges e-bost hon neu unrhyw > atodiadau yn rhydd rhag firysau neu 100% yn ddiogel. Oni bai fod hyn > wedi ei ddatgan yn uniongyrchol yn nhestun yr e-bost, nid bwriad y > neges e-bost hon yw ffurfio contract rhwymol - mae rhestr o lofnodwyr > awdurdodedig ar gael o Swyddfa Cyllid Prifysgol Bangor. > This email and any attachments may contain confidential material and > is solely for the use of the intended recipient(s). If you have > received this email in error, please notify the sender immediately and > delete this email. If you are not the intended recipient(s), you must > not use, retain or disclose any information contained in this email. > Any views or opinions are solely those of the sender and do not > necessarily represent those of Bangor University. Bangor University > does not guarantee that this email or any attachments are free from > viruses or 100% secure. Unless expressly stated in the body of the > text of the email, this email is not intended to form a binding > contract - a list of authorised signatories is available from the > Bangor University Finance Office. > > _______________________________________________ > 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 mkmodi at aau.ac.in Fri Feb 27 00:03:47 2015 From: mkmodi at aau.ac.in (Mahendra Modi) Date: Fri, 27 Feb 2015 10:33:47 +0530 Subject: [Bio-Linux] Bio-linux training at Assam Agricultural University, Jorhat, Assam India Message-ID: We at the Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam India had a week long training on Bio-linux and gene discovery. Tony Travis, Adam Price and Alex Douglas from University of Aberdeen were the resource persons. There were 40 participants from various nooks and corners of North-East India and a few from other parts of India too. The training was very well received and most of the participants installed bio-linux on their computers at the end of the training. We hope to continue similar training events in future too. Mahendra -- ________________________ Prof. Mahendra K Modi Head, Agril Biotechnology & Coordinator, DIC Assam Agricultural University Jorhat 785013, India -------------- next part -------------- An HTML attachment was scrubbed... URL: From papo0009 at gapps.umu.se Fri Feb 27 17:00:18 2015 From: papo0009 at gapps.umu.se (Parham Pourbozorgi) Date: Fri, 27 Feb 2015 23:00:18 +0100 Subject: [Bio-Linux] shared folders disappeared after update Message-ID: Hello all, I have been using biolinux 8 on VMware player 7.1.0 build-2496824. Yesterday after a biolinux (or may be Ubuntu) update the shared folders between VMware and my host (Windows 8.1) disappeared and no matter how many of the online tips I tried and how many times I re-installed the biolinux I couldn't figure out a solution. I was wondering if you know the cause and you can give any advise. I must add that biolinux is a fantastic job and I really appreciate the effort, thanks! Cheers, Parham -------------- next part -------------- An HTML attachment was scrubbed... URL: From parharn at gmail.com Fri Feb 27 16:57:55 2015 From: parharn at gmail.com (Parham) Date: Fri, 27 Feb 2015 22:57:55 +0100 Subject: [Bio-Linux] share folder on vmware player not working Message-ID: Hello all, I have been using biolinux 8 on VMware player 7.1.0 build-2496824. Yesterday after a biolinux (or may be Ubuntu) update the shared folders between VMware and my host (Windows 8.1) disappeared and no matter how many of the online tips I tried and how many times I re-installed the biolinux I couldn't figure out a solution. I was wondering if you know the cause and you can give any advise. I must add that biolinux is a fantastic job and I really appreciate the effort, thanks! Cheers, Parham -------------- next part -------------- An HTML attachment was scrubbed... URL: