From tbooth at ceh.ac.uk  Wed Jun 17 12:30:19 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 17 Jun 2015 17:30:19 +0100
Subject: [Bio-Linux] Bio-Linux 8.0.7
Message-ID: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>

Dear Bio-Linux users,

I've just put out a point release of Bio-Linux 8.  As usual, existing
users of installed systems do not need to do anything to get automatic
package updates but there are a couple of things that might be of
interest if you especially if you are running Bio-Linux as a VM (see 5
and 6).

1)
I've set it so machines installed from this image will install security
patches and basic updates silently and without prompting.  At the moment
you are automatically notified but you have to approve the installation.

If you want to enable this on your existing machine grab this script:
http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
and run it as root:
$ sudo bash unattended_upgrade.sh

Note that this only applies to security updates and updates that don't
change package dependencies.  For other updates you'll still be prompted
to confirm.

2)
The OSwitch package for Docker is installed by default, but you still
need to add Docker to the system to run it.  A Docker set-up script is
provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
See https://github.com/wurmlab/oswitch

I've also added the Stacks package which was previously mentioned on
this list:
http://catchenlab.life.illinois.edu/stacks/

3)
MySQL is no longer on the default image.  Most people don't use it, and
for those who do need it the server can be added back very easily
(apt-get install mysql-server).  Note that Ubuntu also supports
mariadb-server 5.5 if you prefer to use that instead.

4)
I've removed a bunch of redundant 32-bit libs, saving some space and
fixing a dependency conflict issue.  The update manager should also
purge these libraries from existing systems for you.

5) 
VirtualBox now uses the "Paravirtualized" network device by default.
This is much faster for downloads onto the VM and is recommended for all
users.  Shut down your VM then look under Network -> Adapter1 ->
Advanced -> Adapter Type and simply change it to the last option before
booting back up again.

6)
I've increased the HD size on the VirtulBox image to a more useful
100GB.  Under VirtualBox this will only use extra disk space on your
host system if you actually put stuff on the disk, but for other VM
systems it may use up space right away.  There remains no satisfactory
way to increase the main disk size for your existing VMs - you generally
need to add on and format an extra disk as discussed previously on this
list.

And that's it.  Enjoy!

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>

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  Thu Jun 18 04:40:02 2015
From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson)
Date: Thu, 18 Jun 2015 08:40:02 +0000
Subject: [Bio-Linux] Bio-Linux 8.0.7
In-Reply-To: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <7E756F18289AF64B967C333AC3BF70210182420418@MBXP02.ds.man.ac.uk>

The updates sound very helpful.  Has there been any update to the version of Galaxy?

Thanks,
Ian

________________________________________
From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
Sent: 17 June 2015 17:30
To: bio-linux at nebclists.nerc.ac.uk
Subject: [Bio-Linux] Bio-Linux 8.0.7

Dear Bio-Linux users,

I've just put out a point release of Bio-Linux 8.  As usual, existing
users of installed systems do not need to do anything to get automatic
package updates but there are a couple of things that might be of
interest if you especially if you are running Bio-Linux as a VM (see 5
and 6).

1)
I've set it so machines installed from this image will install security
patches and basic updates silently and without prompting.  At the moment
you are automatically notified but you have to approve the installation.

If you want to enable this on your existing machine grab this script:
http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
and run it as root:
$ sudo bash unattended_upgrade.sh

Note that this only applies to security updates and updates that don't
change package dependencies.  For other updates you'll still be prompted
to confirm.

2)
The OSwitch package for Docker is installed by default, but you still
need to add Docker to the system to run it.  A Docker set-up script is
provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
See https://github.com/wurmlab/oswitch

I've also added the Stacks package which was previously mentioned on
this list:
http://catchenlab.life.illinois.edu/stacks/

3)
MySQL is no longer on the default image.  Most people don't use it, and
for those who do need it the server can be added back very easily
(apt-get install mysql-server).  Note that Ubuntu also supports
mariadb-server 5.5 if you prefer to use that instead.

4)
I've removed a bunch of redundant 32-bit libs, saving some space and
fixing a dependency conflict issue.  The update manager should also
purge these libraries from existing systems for you.

5)
VirtualBox now uses the "Paravirtualized" network device by default.
This is much faster for downloads onto the VM and is recommended for all
users.  Shut down your VM then look under Network -> Adapter1 ->
Advanced -> Adapter Type and simply change it to the last option before
booting back up again.

6)
I've increased the HD size on the VirtulBox image to a more useful
100GB.  Under VirtualBox this will only use extra disk space on your
host system if you actually put stuff on the disk, but for other VM
systems it may use up space right away.  There remains no satisfactory
way to increase the main disk size for your existing VMs - you generally
need to add on and format an extra disk as discussed previously on this
list.

And that's it.  Enjoy!

TIM

--
Tim Booth <tbooth at ceh.ac.uk>

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  Thu Jun 18 05:07:55 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 18 Jun 2015 10:07:55 +0100
Subject: [Bio-Linux] Bio-Linux 8.0.7
In-Reply-To: <7E756F18289AF64B967C333AC3BF70210182420418@MBXP02.ds.man.ac.uk>
References: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>
 <7E756F18289AF64B967C333AC3BF70210182420418@MBXP02.ds.man.ac.uk>
Message-ID: <1434618475.30934.95.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Ian,

Sadly not.  It's just too big a job since they changed the way the
configuration works.  I have to construct a package that will switch
from the old system to the new one without breaking the configuration or
losing any data.  It's on my TODO list but it's likely to be near the
end of the year before I have tome to tackle it.  The Galaxy developers
make encouraging noises about wanting to support a package but when I
look for actual help with the work I have no luck.  I think they are
more focussed on having Galaxy as a complete self-contained server
system than something that integrates with other packages on Bio-Linux,
which I guess makes sense from their point of view, but it makes things
hard for me.

Cheers,

TIM

On Thu, 2015-06-18 at 08:40 +0000, Ian Donaldson wrote:
> The updates sound very helpful.  Has there been any update to the version of Galaxy?
> 
> Thanks,
> Ian
> 
> ________________________________________
> From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 17 June 2015 17:30
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] Bio-Linux 8.0.7
> 
> Dear Bio-Linux users,
> 
> I've just put out a point release of Bio-Linux 8.  As usual, existing
> users of installed systems do not need to do anything to get automatic
> package updates but there are a couple of things that might be of
> interest if you especially if you are running Bio-Linux as a VM (see 5
> and 6).
> 
> 1)
> I've set it so machines installed from this image will install security
> patches and basic updates silently and without prompting.  At the moment
> you are automatically notified but you have to approve the installation.
> 
> If you want to enable this on your existing machine grab this script:
> http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
> and run it as root:
> $ sudo bash unattended_upgrade.sh
> 
> Note that this only applies to security updates and updates that don't
> change package dependencies.  For other updates you'll still be prompted
> to confirm.
> 
> 2)
> The OSwitch package for Docker is installed by default, but you still
> need to add Docker to the system to run it.  A Docker set-up script is
> provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
> See https://github.com/wurmlab/oswitch
> 
> I've also added the Stacks package which was previously mentioned on
> this list:
> http://catchenlab.life.illinois.edu/stacks/
> 
> 3)
> MySQL is no longer on the default image.  Most people don't use it, and
> for those who do need it the server can be added back very easily
> (apt-get install mysql-server).  Note that Ubuntu also supports
> mariadb-server 5.5 if you prefer to use that instead.
> 
> 4)
> I've removed a bunch of redundant 32-bit libs, saving some space and
> fixing a dependency conflict issue.  The update manager should also
> purge these libraries from existing systems for you.
> 
> 5)
> VirtualBox now uses the "Paravirtualized" network device by default.
> This is much faster for downloads onto the VM and is recommended for all
> users.  Shut down your VM then look under Network -> Adapter1 ->
> Advanced -> Adapter Type and simply change it to the last option before
> booting back up again.
> 
> 6)
> I've increased the HD size on the VirtulBox image to a more useful
> 100GB.  Under VirtualBox this will only use extra disk space on your
> host system if you actually put stuff on the disk, but for other VM
> systems it may use up space right away.  There remains no satisfactory
> way to increase the main disk size for your existing VMs - you generally
> need to add on and format an extra disk as discussed previously on this
> list.
> 
> And that's it.  Enjoy!
> 
> TIM
> 
> --
> Tim Booth <tbooth at ceh.ac.uk>
> 
> 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 <tbooth at ceh.ac.uk>

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  Thu Jun 18 05:20:29 2015
From: Ian.Donaldson at manchester.ac.uk (Ian Donaldson)
Date: Thu, 18 Jun 2015 09:20:29 +0000
Subject: [Bio-Linux] Bio-Linux 8.0.7
In-Reply-To: <1434618475.30934.95.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>
 <7E756F18289AF64B967C333AC3BF70210182420418@MBXP02.ds.man.ac.uk>,
 <1434618475.30934.95.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <7E756F18289AF64B967C333AC3BF7021018242043F@MBXP02.ds.man.ac.uk>

Thanks, I appreciate the update.  Unfortunately the supplied version cannot cope with installing the dependencies for the tools I need in my tutorials.  But I shall definitely keep an eye out for developments in Bio-Linux.

BTW would it be possible to create a version of the BL-VM as a static drive size, rather than dynamic one?  I am under the impression that read/write access is much slower using a dynamic sized VM.

Ian

________________________________________
From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
Sent: 18 June 2015 10:07
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Bio-Linux 8.0.7

Hi Ian,

Sadly not.  It's just too big a job since they changed the way the
configuration works.  I have to construct a package that will switch
from the old system to the new one without breaking the configuration or
losing any data.  It's on my TODO list but it's likely to be near the
end of the year before I have tome to tackle it.  The Galaxy developers
make encouraging noises about wanting to support a package but when I
look for actual help with the work I have no luck.  I think they are
more focussed on having Galaxy as a complete self-contained server
system than something that integrates with other packages on Bio-Linux,
which I guess makes sense from their point of view, but it makes things
hard for me.

Cheers,

TIM

On Thu, 2015-06-18 at 08:40 +0000, Ian Donaldson wrote:
> The updates sound very helpful.  Has there been any update to the version of Galaxy?
>
> Thanks,
> Ian
>
> ________________________________________
> From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 17 June 2015 17:30
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: [Bio-Linux] Bio-Linux 8.0.7
>
> Dear Bio-Linux users,
>
> I've just put out a point release of Bio-Linux 8.  As usual, existing
> users of installed systems do not need to do anything to get automatic
> package updates but there are a couple of things that might be of
> interest if you especially if you are running Bio-Linux as a VM (see 5
> and 6).
>
> 1)
> I've set it so machines installed from this image will install security
> patches and basic updates silently and without prompting.  At the moment
> you are automatically notified but you have to approve the installation.
>
> If you want to enable this on your existing machine grab this script:
> http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
> and run it as root:
> $ sudo bash unattended_upgrade.sh
>
> Note that this only applies to security updates and updates that don't
> change package dependencies.  For other updates you'll still be prompted
> to confirm.
>
> 2)
> The OSwitch package for Docker is installed by default, but you still
> need to add Docker to the system to run it.  A Docker set-up script is
> provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
> See https://github.com/wurmlab/oswitch
>
> I've also added the Stacks package which was previously mentioned on
> this list:
> http://catchenlab.life.illinois.edu/stacks/
>
> 3)
> MySQL is no longer on the default image.  Most people don't use it, and
> for those who do need it the server can be added back very easily
> (apt-get install mysql-server).  Note that Ubuntu also supports
> mariadb-server 5.5 if you prefer to use that instead.
>
> 4)
> I've removed a bunch of redundant 32-bit libs, saving some space and
> fixing a dependency conflict issue.  The update manager should also
> purge these libraries from existing systems for you.
>
> 5)
> VirtualBox now uses the "Paravirtualized" network device by default.
> This is much faster for downloads onto the VM and is recommended for all
> users.  Shut down your VM then look under Network -> Adapter1 ->
> Advanced -> Adapter Type and simply change it to the last option before
> booting back up again.
>
> 6)
> I've increased the HD size on the VirtulBox image to a more useful
> 100GB.  Under VirtualBox this will only use extra disk space on your
> host system if you actually put stuff on the disk, but for other VM
> systems it may use up space right away.  There remains no satisfactory
> way to increase the main disk size for your existing VMs - you generally
> need to add on and format an extra disk as discussed previously on this
> list.
>
> And that's it.  Enjoy!
>
> TIM
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
>
> 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 <tbooth at ceh.ac.uk>

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  Thu Jun 18 07:05:33 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 18 Jun 2015 12:05:33 +0100
Subject: [Bio-Linux] trouble booting bio linux usb
In-Reply-To: <BAY175-W16ACB184CF750410BDEC7AE1A60@phx.gbl>
References: <BAY175-W16ACB184CF750410BDEC7AE1A60@phx.gbl>
Message-ID: <1434625533.30934.150.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Yessica,

I'm switching your message from "bio-linux-dev" to "bio-linux" as the
discussion list is much more appropriate for this question, and I think
it might be where you intended to post anyway.  Please join the list at:

http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

Sorry to hear you are having trouble getting Bio-Linux to boot, and I'm
glad you are persisting.

You are trying to make a Bio-Linux USB stick on Linux Mint using the
default USB maker tool in Mint.  I've not tried this myself but my guess
is that the Mint USB tool will be quite specific to the version of
SYSLinux being used (that's the thing that makes the USB boot).  That
certainly explains the error you got when trying Bio-Linux 7.  I'm not
sure about Bio-Linux 8 but I suspect it is a similar thing.

Please try using the UNetBootIn tool with the Bio-Linux 8 image.  I
think on recent versions of Mint you will just be able to do "apt-get
install unetbootin" or else you'll have to get it from
http://unetbootin.sourceforge.net/.

Let me know if that works.

Cheers,

TIM




On Wed, 2015-06-17 at 17:38 -0500, yessica Parera wrote:
> Hi everyone! My names is Yessica Parera, Im a master student from
> Universidad Nacional Autonoma de Mexico, now Im doing some research
> about marine actinomycetes, and Im looking forward to use your bio
> linux package, my computer is a  hp laptop with intel corei3, 6 gb on
> ram and currently SO Linux Mint Qiana. I want to use bio linux as my
> new OS. 
> 
> 
> I downloaded the OS Bio linux 8 from your website, and mount it on a
> usb using the option in the menu of mint. 
> After booting my laptop, and selecting the option to boot from usb,
> nothing happens and mi current OS starts normally.
> 
> 
> 
> 
> I tried downloading the Bio linux 7 and booting, but this message
> comes to screen:
> 
> 
> SYSLINUX 3.63 Debian-2008-07-15 EBIOS Copyright (c)1994-2008 H Peter
> Anvin Unknown keyword in configuration file Boot
> 
> 
> Im new usign linux and I apologize for my ingnorance, but I cant thing
> on anythings esle to do. 
> 
> 
> I would really appreciate your help.
> 
> 
> Best regards. 
> 
> 
> 
> 
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

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 Jun 18 07:14:25 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 18 Jun 2015 12:14:25 +0100
Subject: [Bio-Linux] Bio-Linux 8.0.7
In-Reply-To: <7E756F18289AF64B967C333AC3BF7021018242043F@MBXP02.ds.man.ac.uk>
References: <1434558619.30934.81.camel@wllt1771.nerc-wallingford.ac.uk>
 <7E756F18289AF64B967C333AC3BF70210182420418@MBXP02.ds.man.ac.uk>
 , <1434618475.30934.95.camel@wllt1771.nerc-wallingford.ac.uk>
 <7E756F18289AF64B967C333AC3BF7021018242043F@MBXP02.ds.man.ac.uk>
Message-ID: <1434626065.30934.158.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Ian,

The problem here is that it would immediately take up 100GB on every
users machine, which is a bit scary.  Also my impression is that while
writes are slow while the disk is expanding, overwriting and reading are
still fast.

It's reasonably easy to make the switch yourself.  Use the "Virtual
Media Manager" to copy the disk as a fixed-size VDI, then under machine
settings unplug the VMDK disk and connect the new VDI version.

Actually, I think it might even be the case that when you export the
machine as an OVA the disk automatically reverts to a dynamically-sized
VMDK.  I think this might be a feature of the .OVA spec - to be honest I
never tried it.

Cheers,

TIM

> BTW would it be possible to create a version of the BL-VM as a static
> drive size, rather than dynamic one?  I am under the impression that
> read/write access is much slower using a dynamic sized VM.
> 
> Ian
> 
> ________________________________________
> From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
> Sent: 18 June 2015 10:07
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux 8.0.7
> 
> Hi Ian,
> 
> Sadly not.  It's just too big a job since they changed the way the
> configuration works.  I have to construct a package that will switch
> from the old system to the new one without breaking the configuration or
> losing any data.  It's on my TODO list but it's likely to be near the
> end of the year before I have tome to tackle it.  The Galaxy developers
> make encouraging noises about wanting to support a package but when I
> look for actual help with the work I have no luck.  I think they are
> more focussed on having Galaxy as a complete self-contained server
> system than something that integrates with other packages on Bio-Linux,
> which I guess makes sense from their point of view, but it makes things
> hard for me.
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2015-06-18 at 08:40 +0000, Ian Donaldson wrote:
> > The updates sound very helpful.  Has there been any update to the version of Galaxy?
> >
> > Thanks,
> > Ian
> >
> > ________________________________________
> > From: Bio-Linux [bio-linux-bounces at nebclists.nerc.ac.uk] on behalf of Tim Booth [tbooth at ceh.ac.uk]
> > Sent: 17 June 2015 17:30
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: [Bio-Linux] Bio-Linux 8.0.7
> >
> > Dear Bio-Linux users,
> >
> > I've just put out a point release of Bio-Linux 8.  As usual, existing
> > users of installed systems do not need to do anything to get automatic
> > package updates but there are a couple of things that might be of
> > interest if you especially if you are running Bio-Linux as a VM (see 5
> > and 6).
> >
> > 1)
> > I've set it so machines installed from this image will install security
> > patches and basic updates silently and without prompting.  At the moment
> > you are automatically notified but you have to approve the installation.
> >
> > If you want to enable this on your existing machine grab this script:
> > http://nebc.nerc.ac.uk/downloads/bl8_only/unattended_upgrade.sh
> > and run it as root:
> > $ sudo bash unattended_upgrade.sh
> >
> > Note that this only applies to security updates and updates that don't
> > change package dependencies.  For other updates you'll still be prompted
> > to confirm.
> >
> > 2)
> > The OSwitch package for Docker is installed by default, but you still
> > need to add Docker to the system to run it.  A Docker set-up script is
> > provided under /usr/share/oswitch/contrib/docker_setup_ubuntu.sh
> > See https://github.com/wurmlab/oswitch
> >
> > I've also added the Stacks package which was previously mentioned on
> > this list:
> > http://catchenlab.life.illinois.edu/stacks/
> >
> > 3)
> > MySQL is no longer on the default image.  Most people don't use it, and
> > for those who do need it the server can be added back very easily
> > (apt-get install mysql-server).  Note that Ubuntu also supports
> > mariadb-server 5.5 if you prefer to use that instead.
> >
> > 4)
> > I've removed a bunch of redundant 32-bit libs, saving some space and
> > fixing a dependency conflict issue.  The update manager should also
> > purge these libraries from existing systems for you.
> >
> > 5)
> > VirtualBox now uses the "Paravirtualized" network device by default.
> > This is much faster for downloads onto the VM and is recommended for all
> > users.  Shut down your VM then look under Network -> Adapter1 ->
> > Advanced -> Adapter Type and simply change it to the last option before
> > booting back up again.
> >
> > 6)
> > I've increased the HD size on the VirtulBox image to a more useful
> > 100GB.  Under VirtualBox this will only use extra disk space on your
> > host system if you actually put stuff on the disk, but for other VM
> > systems it may use up space right away.  There remains no satisfactory
> > way to increase the main disk size for your existing VMs - you generally
> > need to add on and format an extra disk as discussed previously on this
> > list.
> >
> > And that's it.  Enjoy!
> >
> > TIM
> >
> > --
> > Tim Booth <tbooth at ceh.ac.uk>
> >
> > 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 <tbooth at ceh.ac.uk>
> 
> 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 <tbooth at ceh.ac.uk>

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 paumarc at gmail.com  Fri Jun 19 06:04:54 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Fri, 19 Jun 2015 12:04:54 +0200
Subject: [Bio-Linux] Rapidir R-cran package
Message-ID: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>

Hello9 everybody.

 I'm, interested to install R-cran package on my system, nevertheless i do
not find it at repositories neither in bioconductor

i look at R-cram web page for Rapidir , and i have not found any linux
binary.

http://cran.r-project.org/web/packages/RAPIDR/index.html

Can some one told me if it is possible to install it in  biolinux?

thanks

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
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From tony.travis at minke-informatics.co.uk  Fri Jun 19 06:41:43 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Fri, 19 Jun 2015 11:41:43 +0100
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
Message-ID: <5583F1E7.2010205@minke-informatics.co.uk>

On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
> Hello9 everybody.
> 
>  I'm, interested to install R-cran package on my system, nevertheless i
> do not find it at repositories neither in bioconductor
> 
> i look at R-cram web page for Rapidir , and i have not found any linux
> binary.
> 
> http://cran.r-project.org/web/packages/RAPIDR/index.html
> 
> Can some one told me if it is possible to install it in  biolinux?

Hi, Pau Marc.

The CRAN package "RAPIDR" requires a BioConductor package
"GenomicAlignments", which must be installed first. See:

> http://cran.r-project.org/web/packages/RAPIDR/index.html
> http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf

This is how to install and load "RAPIDR" in Bio-Linux 8:

  R
  source("http://bioconductor.org/biocLite.R")
  biocLite("GenomicAlignments")
  install.packages("RAPIDR")
  library(RAPIDR)

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




From tbooth at ceh.ac.uk  Fri Jun 19 07:19:23 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 19 Jun 2015 12:19:23 +0100
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <5583F1E7.2010205@minke-informatics.co.uk>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
Message-ID: <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Pau Marc,

On Bio-Linux 8 you can install all packages from the big auto-generated
C2D4U repository via apt-get, so for example you can do:

apt-get install r-bioc-genomicalignments

However, RAPIDR is missing, so for now you have to install it via
install.packages() and update it manually as Tony suggested.

I'll look into adding a package for this myself.  Its normally very easy
to do.

Cheers,

TIM

On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
> On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
> > Hello9 everybody.
> > 
> >  I'm, interested to install R-cran package on my system, nevertheless i
> > do not find it at repositories neither in bioconductor
> > 
> > i look at R-cram web page for Rapidir , and i have not found any linux
> > binary.
> > 
> > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > 
> > Can some one told me if it is possible to install it in  biolinux?
> 
> Hi, Pau Marc.
> 
> The CRAN package "RAPIDR" requires a BioConductor package
> "GenomicAlignments", which must be installed first. See:
> 
> > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
> 
> This is how to install and load "RAPIDR" in Bio-Linux 8:
> 
>   R
>   source("http://bioconductor.org/biocLite.R")
>   biocLite("GenomicAlignments")
>   install.packages("RAPIDR")
>   library(RAPIDR)
> 
> HTH,
> 
>   Tony.
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>

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 tony.travis at abdn.ac.uk  Fri Jun 19 07:32:37 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Fri, 19 Jun 2015 12:32:37 +0100
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <5583FDD5.1060402@abdn.ac.uk>

On 19/06/15 12:19, Tim Booth wrote:
> Hi Pau Marc,
>
> On Bio-Linux 8 you can install all packages from the big auto-generated
> C2D4U repository via apt-get, so for example you can do:
>
> apt-get install r-bioc-genomicalignments

Hi, Tim.

Sorry, I'm out of date: I'd not realised that someone else carried on
with C2D after me and Steffan gave up trying to package Bioconductor!

Very useful to know that Bioconductor is packaged automatically now
because THAT was one of the BIG things on my Bio-Linux wish-list :-)

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 paumarc at gmail.com  Fri Jun 19 10:59:38 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Fri, 19 Jun 2015 16:59:38 +0200
Subject: [Bio-Linux] Rapidir R-cran package
In-Reply-To: <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CADFuJLhpoMWebFEwoMFqfquFgiREsavQKmD=7FaJrahR1cZGbQ@mail.gmail.com>
 <5583F1E7.2010205@minke-informatics.co.uk>
 <1434712763.30934.201.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CADFuJLhavnBkOpiC675fZCrwO1yOUTpm5jnwttP3cZJ_z7s4Aw@mail.gmail.com>

Thanks

P
El 19/06/2015 13:19, "Tim Booth" <tbooth at ceh.ac.uk> escribi?:

> Hi Pau Marc,
>
> On Bio-Linux 8 you can install all packages from the big auto-generated
> C2D4U repository via apt-get, so for example you can do:
>
> apt-get install r-bioc-genomicalignments
>
> However, RAPIDR is missing, so for now you have to install it via
> install.packages() and update it manually as Tony suggested.
>
> I'll look into adding a package for this myself.  Its normally very easy
> to do.
>
> Cheers,
>
> TIM
>
> On Fri, 2015-06-19 at 11:41 +0100, Tony Travis wrote:
> > On 19/06/15 11:04, Pau Marc Mu?oz Torres wrote:
> > > Hello9 everybody.
> > >
> > >  I'm, interested to install R-cran package on my system, nevertheless i
> > > do not find it at repositories neither in bioconductor
> > >
> > > i look at R-cram web page for Rapidir , and i have not found any linux
> > > binary.
> > >
> > > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > >
> > > Can some one told me if it is possible to install it in  biolinux?
> >
> > Hi, Pau Marc.
> >
> > The CRAN package "RAPIDR" requires a BioConductor package
> > "GenomicAlignments", which must be installed first. See:
> >
> > > http://cran.r-project.org/web/packages/RAPIDR/index.html
> > >
> http://www.bioconductor.org/packages/release/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf
> >
> > This is how to install and load "RAPIDR" in Bio-Linux 8:
> >
> >   R
> >   source("http://bioconductor.org/biocLite.R")
> >   biocLite("GenomicAlignments")
> >   install.packages("RAPIDR")
> >   library(RAPIDR)
> >
> > HTH,
> >
> >   Tony.
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
>
> 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
>
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From ramendra.sarma at gmail.com  Tue Jun 23 00:09:01 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Tue, 23 Jun 2015 09:39:01 +0530
Subject: [Bio-Linux] ibus
Message-ID: <CAP3xa23nxb9+9xm0Tgu9j+1wcREobtbMMWOxESYAX7gM+XgpLA@mail.gmail.com>

Hi,
Why ibus is not shown when I type it after clicking the icon of search at
the top right of ubuntu desktop?

-- 
----------------------------------------------------------------------------------------------------------------------------------------






*Dr R N SarmaProfessorDepartment of Plant Breeding and GeneticsAssam
Agricultural UniversityJorhat-785013Assam, Indiaweb: www.aau.ac.in;
<http://www.aaau.ac.in> Phone: +91-376-2310526; +91-376231133(R);
9435350529(M)*
--------------------------------------------------------------------------------------------------------------------------
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From tony.travis at minke-informatics.co.uk  Tue Jun 23 04:55:25 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Tue, 23 Jun 2015 09:55:25 +0100
Subject: [Bio-Linux] ibus
In-Reply-To: <CAP3xa23nxb9+9xm0Tgu9j+1wcREobtbMMWOxESYAX7gM+XgpLA@mail.gmail.com>
References: <CAP3xa23nxb9+9xm0Tgu9j+1wcREobtbMMWOxESYAX7gM+XgpLA@mail.gmail.com>
Message-ID: <55891EFD.8020803@minke-informatics.co.uk>

On 23/06/15 05:09, Ramendra Sarma wrote:
> Hi,
> Why ibus is not shown when I type it after clicking the icon of search
> at the top right of ubuntu desktop?

Hi, Ramen.

Do you mean the "Dash" icon at the top left?

The reason is that "ibus" is a command-line program - To find it use:

  which -a ibus

Or:

  dpkg -L ibus

The program is:

  /usr/bin/ibus

Documentation is available in the manual page:

  man ibus

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From ikang at inha.ac.kr  Tue Jun 30 02:58:18 2015
From: ikang at inha.ac.kr (Ilnam Kang)
Date: Tue, 30 Jun 2015 15:58:18 +0900
Subject: [Bio-Linux] How can I access Galaxy on a Bio-Linux server over the
	network?
Message-ID: <CAMZGg2Cbx_EPPbyTFrZh6zwkZnBA1sj-HmNScK13L7A+uvE2Rg@mail.gmail.com>

Dear,

I'm using Bio Linux 8 server for my work and I'd like to access Galaxy on
my Bio Linux server from my laptop (OS: Windows) over the network via a web
browser.

I tried editing "00_upstream.ini" file in
/etc/galaxy-server/universe_wsgi.d directory. Specifically, as explained in
the file, I changed host from 127.0.0.1 to 0.0.0.0 and restarted galaxy.
But, still I couldn't access galaxy from my laptop. It seems that the
change had an effect within the server: Galaxy could be accessed through
IP_address:8080 as well as localhost:8080 within the server itself.

What should I do to access Galaxy on my Bio-Linux server from my laptop
over the network?

Thanks.

Sincerely,

----
Ilnam Kang
Postdoctoral researcher
Division of Biology and Ocean Sciences
Inha University
Yonghyun dong 253, Incheon 402-751
Republic of Korea (South Korea)
Tel: +82-32-876-5541, Mobile: +82-10-6232-1701
e-mail: ikang at inha.ac.kr
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From tbooth at ceh.ac.uk  Tue Jun 30 04:57:57 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 30 Jun 2015 09:57:57 +0100
Subject: [Bio-Linux] How can I access Galaxy on a Bio-Linux server over
 the network?
In-Reply-To: <CAMZGg2Cbx_EPPbyTFrZh6zwkZnBA1sj-HmNScK13L7A+uvE2Rg@mail.gmail.com>
References: <CAMZGg2Cbx_EPPbyTFrZh6zwkZnBA1sj-HmNScK13L7A+uvE2Rg@mail.gmail.com>
Message-ID: <1435654677.5192.134.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

The relevant information on Galaxy is all here:

http://environmentalomics.org/bio-linux-galaxy/

See the section near the bottom.  You need to change the firewall
configuration on the machine using the icon under System Settings, of if
you are going over an insecure network you should use SSH port
tunnelling.

Best,

TIM

On Tue, 2015-06-30 at 15:58 +0900, Ilnam Kang wrote:
> Dear,
> 
> 
> I'm using Bio Linux 8 server for my work and I'd like to access Galaxy
> on my Bio Linux server from my laptop (OS: Windows) over the network
> via a web browser.
> 
> 
> I tried editing "00_upstream.ini" file
> in /etc/galaxy-server/universe_wsgi.d directory. Specifically, as
> explained in the file, I changed host from 127.0.0.1 to 0.0.0.0 and
> restarted galaxy. But, still I couldn't access galaxy from my laptop.
> It seems that the change had an effect within the server: Galaxy could
> be accessed through IP_address:8080 as well as localhost:8080 within
> the server itself.
> 
> 
> What should I do to access Galaxy on my Bio-Linux server from my
> laptop over the network?
> 
> 
> 
> Thanks.
> 
> 
> Sincerely,
> 
> 
> ----
> Ilnam Kang
> Postdoctoral researcher
> Division of Biology and Ocean Sciences
> Inha University
> Yonghyun dong 253, Incheon 402-751
> Republic of Korea (South Korea)
> Tel: +82-32-876-5541, Mobile: +82-10-6232-1701
> e-mail: ikang at inha.ac.kr
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
Tim Booth <tbooth at ceh.ac.uk>

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 paumarc at gmail.com  Tue Jun 30 06:45:52 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Tue, 30 Jun 2015 12:45:52 +0200
Subject: [Bio-Linux] R libraries version
Message-ID: <CADFuJLhUV8d8EKt48NRoDeE+_EjH96=095XN66+9nm2vd8Ganw@mail.gmail.com>

Hello everybody

 As you know i working with Rapidir, i finally could install it correctly,
reading the software documentation i found that it requires the library
GenomicRanges_1.14.4 and biolinux has GenomicRanges_1.20.5 . It is due to
the fact that after GenomicRanges_1.14.4 the function SummarizeOverlaps has
moved to a another package

 some body knows how i could deal with it? is any possibility to indicate
where is know this function or use the old library?

Thanks

Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
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From briancady101 at yahoo.com  Tue Jun 30 08:10:54 2015
From: briancady101 at yahoo.com (Brian Cady)
Date: Tue, 30 Jun 2015 12:10:54 +0000 (UTC)
Subject: [Bio-Linux] R libraries version
In-Reply-To: <CADFuJLhUV8d8EKt48NRoDeE+_EjH96=095XN66+9nm2vd8Ganw@mail.gmail.com>
References: <CADFuJLhUV8d8EKt48NRoDeE+_EjH96=095XN66+9nm2vd8Ganw@mail.gmail.com>
Message-ID: <1171662822.1208933.1435666254984.JavaMail.yahoo@mail.yahoo.com>

Hi Pau,
 Where did SummarizeOverlaps move to? Maybe you could use it there.

Brian

     On Tuesday, June 30, 2015 6:45 AM, Pau Marc Mu?oz Torres <paumarc at gmail.com> wrote:
   

 Hello everybody
?As you know i working with Rapidir, i finally could install it correctly, reading the software documentation i found that it requires the library GenomicRanges_1.14.4 and biolinux has?GenomicRanges_1.20.5 . It is due to the fact that after GenomicRanges_1.14.4 the function SummarizeOverlaps has moved to a another package
?some body knows how i could deal with it? is any possibility to indicate where is know this function or use the old library?
Thanks?
Pau Marc Mu?oz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/


_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


  
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