From tbooth at ceh.ac.uk  Thu Oct  1 06:12:09 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 01 Oct 2015 11:12:09 +0100
Subject: [Bio-Linux] r-cran-ape
In-Reply-To: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>
References: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>
Message-ID: <1443694329.14007.57.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Carlos,

You should have the package available.  On Bio-Linux 8 (Trusty) a bunch
of R packages are provided by the C2D4U PPA repository.  So on my system
I can check it like this:

tbooth at balisaur[tbooth] apt-cache policy r-cran-ape
r-cran-ape:
  Installed: 3.3-1cran1ppa0
  Candidate: 3.3-1cran1ppa0
  Version table:
 *** 3.3-1cran1ppa0 0
        500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/ trusty/main amd64 Packages
        100 /var/lib/dpkg/status

If you installed Bio-Linux 8 directly or ran the upgrade8.sh script then
this should have been set up for you, so either something has gone wrong
or you have set up your software sources manually.

I'd suggest you either re-run the upgrade script to add the repository
configuration or else see
https://launchpad.net/~marutter/+archive/ubuntu/c2d4u and follow the
instructions for manually adding the repository.  Note that you will
also need to set up R core updates in order for these packages to work
properly.

Cheers,

TIM

On Wed, 2015-09-30 at 17:31 -0300, Carlos Morais wrote:
> Hi,
> 
> 
>    Any reason why package r-cran-ape is not present in trusty? It is
> on precise.
> 
> 
> Regards,
> 
>     Carlos
> 
> _______________________________________________
> 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 xavier.depedro at vhir.org  Thu Oct  1 06:14:43 2015
From: xavier.depedro at vhir.org (Xavier de Pedro)
Date: Thu, 1 Oct 2015 12:14:43 +0200
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <560A890A.10506@minke-informatics.co.uk>
References: <5609477B.3060202@vhir.org>
 <560A66A3.5010301@minke-informatics.co.uk> <560A6B91.7010101@vhir.org>
 <560A890A.10506@minke-informatics.co.uk>
Message-ID: <560D0793.7080803@vhir.org>

Thanks Tony!

Thanks was the key information: I re-visited old attempts to connect to
the virtual machine through ssh and this time I managed to do so with
some port forwarding magic. Therefore, it works the solution using just
sandard X2Go ssh access (through a different port)!

Thanks for the hint

Xavier


El 29/09/15 a les 14:50, Tony Travis ha escrit:
> On 29/09/15 12:44, Xavier de Pedro wrote:
>> He he, I presumed that this was going to be an answer. We are using
>> already X2Go in the production server (where we did start the virtualbox
>> machine with BioLinux), and I am still reluctant (feeling lazy and
>> conservative, maybe) to setup everything by hand there, since it might
>> interfere with other customizations we have in that production server
>> (and it took a while to have the whole thing working as intended; if
>> curious, ISPConfig3 setup with ssh-jailkit enabled in that server also).
>>
>> I'm seriously considering that option, again (X2Go to url server and add
>> the biolinux repos, system upgrade, analyse the upgrade sh script for
>> biolinux I saw somewhere a few days ago, etc) , if I can't find another
>> less-risky solution (the RDP to a virtualbox-contained BioLinux server
>> seemed the safest approach for our case).
> Hi, Xavier.
>
> If you can SSH into the VM, then you can use "x2go" to connect to it.
>
> HTH,
>
>   Tony.
>




From morais at iq.usp.br  Thu Oct  1 11:37:23 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Thu, 1 Oct 2015 12:37:23 -0300
Subject: [Bio-Linux] r-cran-ape
In-Reply-To: <1443694329.14007.57.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>
 <1443694329.14007.57.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7nbBk8dQpON=auSmQ413F-fy9U+GjxQFGw8A5ekX9fZ=1Q@mail.gmail.com>

Hi Tim,

    I've added manually the Biolinux ppa. Adding also C2D4U ppa fixes.
Thanks a lot.
    Does the mentioned upgrade script add any other useful repository?

Regards,
    Carlos

On Thu, Oct 1, 2015 at 7:12 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Carlos,
>
> You should have the package available.  On Bio-Linux 8 (Trusty) a bunch
> of R packages are provided by the C2D4U PPA repository.  So on my system
> I can check it like this:
>
> tbooth at balisaur[tbooth] apt-cache policy r-cran-ape
> r-cran-ape:
>   Installed: 3.3-1cran1ppa0
>   Candidate: 3.3-1cran1ppa0
>   Version table:
>  *** 3.3-1cran1ppa0 0
>         500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/ trusty/main
> amd64 Packages
>         100 /var/lib/dpkg/status
>
> If you installed Bio-Linux 8 directly or ran the upgrade8.sh script then
> this should have been set up for you, so either something has gone wrong
> or you have set up your software sources manually.
>
> I'd suggest you either re-run the upgrade script to add the repository
> configuration or else see
> https://launchpad.net/~marutter/+archive/ubuntu/c2d4u and follow the
> instructions for manually adding the repository.  Note that you will
> also need to set up R core updates in order for these packages to work
> properly.
>
> Cheers,
>
> TIM
>
> On Wed, 2015-09-30 at 17:31 -0300, Carlos Morais wrote:
> > Hi,
> >
> >
> >    Any reason why package r-cran-ape is not present in trusty? It is
> > on precise.
> >
> >
> > Regards,
> >
> >     Carlos
> >
> > _______________________________________________
> > 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
>
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From tbooth at ceh.ac.uk  Thu Oct  1 11:47:53 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 01 Oct 2015 16:47:53 +0100
Subject: [Bio-Linux] r-cran-ape
In-Reply-To: <CAAzi7nbBk8dQpON=auSmQ413F-fy9U+GjxQFGw8A5ekX9fZ=1Q@mail.gmail.com>
References: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>
 <1443694329.14007.57.camel@wllt1771.nerc-wallingford.ac.uk>
 <CAAzi7nbBk8dQpON=auSmQ413F-fy9U+GjxQFGw8A5ekX9fZ=1Q@mail.gmail.com>
Message-ID: <1443714473.14007.131.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Carlos,

See for yourself.  You can unpack the upgrade script to view it, but
I've also attached an unpacked copy to this mail for you.  If you read
from line 154 you can see exactly what is being added.  You'll see why I
don't advise people to do this manually as there are many steps.

Cheers,

TIM

On Thu, 2015-10-01 at 12:37 -0300, Carlos Morais wrote:
> Hi Tim,
> 
> 
>     I've added manually the Biolinux ppa. Adding also C2D4U ppa fixes.
> Thanks a lot.
> 
>     Does the mentioned upgrade script add any other useful repository?
> 
> 
> Regards,
> 
>     Carlos
> 
> 
> On Thu, Oct 1, 2015 at 7:12 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>         Hi Carlos,
>         
>         You should have the package available.  On Bio-Linux 8
>         (Trusty) a bunch
>         of R packages are provided by the C2D4U PPA repository.  So on
>         my system
>         I can check it like this:
>         
>         tbooth at balisaur[tbooth] apt-cache policy r-cran-ape
>         r-cran-ape:
>           Installed: 3.3-1cran1ppa0
>           Candidate: 3.3-1cran1ppa0
>           Version table:
>          *** 3.3-1cran1ppa0 0
>                 500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/
>         trusty/main amd64 Packages
>                 100 /var/lib/dpkg/status
>         
>         If you installed Bio-Linux 8 directly or ran the upgrade8.sh
>         script then
>         this should have been set up for you, so either something has
>         gone wrong
>         or you have set up your software sources manually.
>         
>         I'd suggest you either re-run the upgrade script to add the
>         repository
>         configuration or else see
>         https://launchpad.net/~marutter/+archive/ubuntu/c2d4u and
>         follow the
>         instructions for manually adding the repository.  Note that
>         you will
>         also need to set up R core updates in order for these packages
>         to work
>         properly.
>         
>         Cheers,
>         
>         TIM
>         
>         On Wed, 2015-09-30 at 17:31 -0300, Carlos Morais wrote:
>         > Hi,
>         >
>         >
>         >    Any reason why package r-cran-ape is not present in
>         trusty? It is
>         > on precise.
>         >
>         >
>         > Regards,
>         >
>         >     Carlos
>         >
>         
>         > _______________________________________________
>         > 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



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From morais at iq.usp.br  Thu Oct  1 11:53:57 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Thu, 1 Oct 2015 12:53:57 -0300
Subject: [Bio-Linux] r-cran-ape
In-Reply-To: <1443714473.14007.131.camel@wllt1771.nerc-wallingford.ac.uk>
References: <CAAzi7nYfcfESqcX85WaHepYvu9x4m0tghcd17+mR2T5WyaUYKQ@mail.gmail.com>
 <1443694329.14007.57.camel@wllt1771.nerc-wallingford.ac.uk>
 <CAAzi7nbBk8dQpON=auSmQ413F-fy9U+GjxQFGw8A5ekX9fZ=1Q@mail.gmail.com>
 <1443714473.14007.131.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7nYvXCtf0e3yy4S=3dcFBb8UbuYCrkLYcbEcYB0rtjhg3Q@mail.gmail.com>

Ok, thanks again.

On Thu, Oct 1, 2015 at 12:47 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Carlos,
>
> See for yourself.  You can unpack the upgrade script to view it, but
> I've also attached an unpacked copy to this mail for you.  If you read
> from line 154 you can see exactly what is being added.  You'll see why I
> don't advise people to do this manually as there are many steps.
>
> Cheers,
>
> TIM
>
> On Thu, 2015-10-01 at 12:37 -0300, Carlos Morais wrote:
> > Hi Tim,
> >
> >
> >     I've added manually the Biolinux ppa. Adding also C2D4U ppa fixes.
> > Thanks a lot.
> >
> >     Does the mentioned upgrade script add any other useful repository?
> >
> >
> > Regards,
> >
> >     Carlos
> >
> >
> > On Thu, Oct 1, 2015 at 7:12 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> >         Hi Carlos,
> >
> >         You should have the package available.  On Bio-Linux 8
> >         (Trusty) a bunch
> >         of R packages are provided by the C2D4U PPA repository.  So on
> >         my system
> >         I can check it like this:
> >
> >         tbooth at balisaur[tbooth] apt-cache policy r-cran-ape
> >         r-cran-ape:
> >           Installed: 3.3-1cran1ppa0
> >           Candidate: 3.3-1cran1ppa0
> >           Version table:
> >          *** 3.3-1cran1ppa0 0
> >                 500 http://ppa.launchpad.net/marutter/c2d4u/ubuntu/
> >         trusty/main amd64 Packages
> >                 100 /var/lib/dpkg/status
> >
> >         If you installed Bio-Linux 8 directly or ran the upgrade8.sh
> >         script then
> >         this should have been set up for you, so either something has
> >         gone wrong
> >         or you have set up your software sources manually.
> >
> >         I'd suggest you either re-run the upgrade script to add the
> >         repository
> >         configuration or else see
> >         https://launchpad.net/~marutter/+archive/ubuntu/c2d4u and
> >         follow the
> >         instructions for manually adding the repository.  Note that
> >         you will
> >         also need to set up R core updates in order for these packages
> >         to work
> >         properly.
> >
> >         Cheers,
> >
> >         TIM
> >
> >         On Wed, 2015-09-30 at 17:31 -0300, Carlos Morais wrote:
> >         > Hi,
> >         >
> >         >
> >         >    Any reason why package r-cran-ape is not present in
> >         trusty? It is
> >         > on precise.
> >         >
> >         >
> >         > Regards,
> >         >
> >         >     Carlos
> >         >
> >
> >         > _______________________________________________
> >         > 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
>
>
>
>
> Your attachment [upgrade_to_8.sh] was deleted by Fusemail, either because
> it contains either a banned file type, an executable file, or a .zip file
> with an executable file inside it.
> If you would like this investigating please contact the RTS Service Desk
> at rtsservicedesk at nerc.ac.uk
>
> _______________________________________________
> 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 Christopher.Dubay at providence.org  Thu Oct  1 12:42:49 2015
From: Christopher.Dubay at providence.org (Dubay, Christopher J)
Date: Thu, 1 Oct 2015 16:42:49 +0000
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <560D0793.7080803@vhir.org>
References: <5609477B.3060202@vhir.org>
 <560A66A3.5010301@minke-informatics.co.uk> <560A6B91.7010101@vhir.org>
 <560A890A.10506@minke-informatics.co.uk> <560D0793.7080803@vhir.org>
Message-ID: <3F9E65788480CD4282B12895264CC2143C31E1B7@WN35105.or.providence.org>

Would you please share your 'magic' as this may be of interest to the group?

CD

-----Original Message-----
From: Bio-Linux [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Xavier de Pedro
Sent: Thursday, October 01, 2015 3:15 AM
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Several concurrent users to BioLinux8 as Headless VM on Ubuntu14.04?

Thanks Tony!

Thanks was the key information: I re-visited old attempts to connect to the virtual machine through ssh and this time I managed to do so with some port forwarding magic. Therefore, it works the solution using just sandard X2Go ssh access (through a different port)!

Thanks for the hint

Xavier


El 29/09/15 a les 14:50, Tony Travis ha escrit:
> On 29/09/15 12:44, Xavier de Pedro wrote:
>> He he, I presumed that this was going to be an answer. We are using
>> already X2Go in the production server (where we did start the
>> virtualbox machine with BioLinux), and I am still reluctant (feeling
>> lazy and conservative, maybe) to setup everything by hand there,
>> since it might interfere with other customizations we have in that
>> production server (and it took a while to have the whole thing
>> working as intended; if curious, ISPConfig3 setup with ssh-jailkit enabled in that server also).
>>
>> I'm seriously considering that option, again (X2Go to url server and
>> add the biolinux repos, system upgrade, analyse the upgrade sh script
>> for biolinux I saw somewhere a few days ago, etc) , if I can't find
>> another less-risky solution (the RDP to a virtualbox-contained
>> BioLinux server seemed the safest approach for our case).
> Hi, Xavier.
>
> If you can SSH into the VM, then you can use "x2go" to connect to it.
>
> HTH,
>
>   Tony.
>


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

________________________________

This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.


From tbooth at ceh.ac.uk  Thu Oct  1 14:21:26 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 01 Oct 2015 19:21:26 +0100
Subject: [Bio-Linux] Several concurrent users to BioLinux8 as Headless
 VM on Ubuntu14.04?
In-Reply-To: <3F9E65788480CD4282B12895264CC2143C31E1B7@WN35105.or.providence.org>
References: <5609477B.3060202@vhir.org>
 <560A66A3.5010301@minke-informatics.co.uk> <560A6B91.7010101@vhir.org>
 <560A890A.10506@minke-informatics.co.uk> <560D0793.7080803@vhir.org>
 <3F9E65788480CD4282B12895264CC2143C31E1B7@WN35105.or.providence.org>
Message-ID: <1443723686.14007.154.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

I missed this discussion earlier as I was off on leave.  I realised I
had some notes of my own so I have added these to the page on remote
access:

http://environmentalomics.org/bio-linux-remote-access

The main caveat here is that the default VM you download from the
website is set with the admin password as "manager".  This is, IMO,
perfectly reasonable for a VM being run on a personal PC, but as soon as
you start playing with port forwarding it is very easy to open a big
security hole.  Automated attacks scan the internet for machines with
this kind of username and password combo and turn the victims into
botnet zombies!

This especially applies on laptops which may be on a secured local
network most of the time but will then be connected to public WiFi when
they are out and about.

Restricting the "Host IP" to 12.0.0.1 is what most people want to keep
out the baddies, but for Xavier I imagine he left both IP boxes blank
(or equivalently 0.0.0.0) meaning all traffic from anywhere gets routed
through and the VM can be accessed just like a real server.  Bridged
networking could also be an option and you'd probably need it for XRDP
but for this scenario with x2go it's not necessary.

Cheers,

TIM

On Thu, 2015-10-01 at 16:42 +0000, Dubay, Christopher J wrote:
> Would you please share your 'magic' as this may be of interest to the group?
> 
> CD
> 
> -----Original Message-----
> From: Bio-Linux [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Xavier de Pedro
> Sent: Thursday, October 01, 2015 3:15 AM
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] Several concurrent users to BioLinux8 as Headless VM on Ubuntu14.04?
> 
> Thanks Tony!
> 
> Thanks was the key information: I re-visited old attempts to connect to the virtual machine through ssh and this time I managed to do so with some port forwarding magic. Therefore, it works the solution using just sandard X2Go ssh access (through a different port)!
> 
> Thanks for the hint
> 
> Xavier
> 
> 
> El 29/09/15 a les 14:50, Tony Travis ha escrit:
> > On 29/09/15 12:44, Xavier de Pedro wrote:
> >> He he, I presumed that this was going to be an answer. We are using
> >> already X2Go in the production server (where we did start the
> >> virtualbox machine with BioLinux), and I am still reluctant (feeling
> >> lazy and conservative, maybe) to setup everything by hand there,
> >> since it might interfere with other customizations we have in that
> >> production server (and it took a while to have the whole thing
> >> working as intended; if curious, ISPConfig3 setup with ssh-jailkit enabled in that server also).
> >>
> >> I'm seriously considering that option, again (X2Go to url server and
> >> add the biolinux repos, system upgrade, analyse the upgrade sh script
> >> for biolinux I saw somewhere a few days ago, etc) , if I can't find
> >> another less-risky solution (the RDP to a virtualbox-contained
> >> BioLinux server seemed the safest approach for our case).
> > Hi, Xavier.
> >
> > If you can SSH into the VM, then you can use "x2go" to connect to it.
> >
> > HTH,
> >
> >   Tony.
> >
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> ________________________________
> 
> This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message.
> _______________________________________________
> 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 juls.jaeger at gmx.de  Thu Oct  1 20:28:51 2015
From: juls.jaeger at gmx.de (Julian Jaeger)
Date: Fri, 02 Oct 2015 01:28:51 +0100
Subject: [Bio-Linux] Cannot upload files to data library
Message-ID: <1443745731.3236.12.camel@julS-RV01>

Hi everyone, 

I just received my RNAseq data but now I have problems to upload the
fastq files to my data library. 

I created an admin account and want to upload the files in a data
library via 'Upload files from filesystem paths' with the option 'Link
to files without copying into galaxy'. 
(My primary drive is to small for all files, so I want to keep them on
my secondary harddrive). 

However Galaxy claims an invalid path, because it always adds
'/usr/lib/galaxy-server' to every path that I enter. 

I also tried to upload the files without linking, but it doesn't work
either. 

I have not found any answers in the www, so I hope someone can help me
out with my (probably minor) problem.

Many thanks, Julian




From jaeger.julian at gmx.net  Thu Oct  1 20:37:54 2015
From: jaeger.julian at gmx.net (jaeger.julian at gmx.net)
Date: Fri, 2 Oct 2015 01:37:54 +0100
Subject: [Bio-Linux] Cannot upload files to data library
In-Reply-To: <1443745731.3236.12.camel@julS-RV01>
References: <1443745731.3236.12.camel@julS-RV01>
Message-ID: <000201d0fcaa$94765fd0$bd631f70$@gmx.net>


Hi everyone, 

I just received my RNAseq data but now I have problems to upload the fastq files to my data library. 

I created an admin account and want to upload the files in a data library via 'Upload files from filesystem paths' with the option 'Link to files without copying into galaxy'. 
(My primary drive is to small for all files, so I want to keep them on my secondary harddrive). 

However Galaxy claims an invalid path, because it always adds '/usr/lib/galaxy-server' to every path that I enter. 

I also tried to upload the files without linking, but it doesn't work either. 

I have not found any answers in the www, so I hope someone can help me out with my (probably minor) problem.

Many thanks, Julian





From morais at iq.usp.br  Mon Oct  5 14:59:13 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Mon, 5 Oct 2015 15:59:13 -0300
Subject: [Bio-Linux] CheckM
In-Reply-To: <CAAzi7nZ_J_qDRc_jjtpZ2Xo5bTNd8pMgwzn0iP5VNsvp91ybOA@mail.gmail.com>
References: <CAAzi7nZ_J_qDRc_jjtpZ2Xo5bTNd8pMgwzn0iP5VNsvp91ybOA@mail.gmail.com>
Message-ID: <CAAzi7naO1UtSmW4Cp-1H0ArvJD00WPmaFykJhya0jgVSC04iTw@mail.gmail.com>

E quanto ao AntiSmash
<http://antismash.secondarymetabolites.org/download.html>?

On Mon, Oct 5, 2015 at 2:25 PM, Carlos Morais <morais at iq.usp.br> wrote:

> Hi,
>
>     Is in anyone plans to make CheckM
> <https://ecogenomics.github.io/CheckM/> available on BioLinux?
>
> Regards,
>     Carlos
>
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From morais at iq.usp.br  Mon Oct  5 15:00:34 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Mon, 5 Oct 2015 16:00:34 -0300
Subject: [Bio-Linux] CheckM
In-Reply-To: <CAAzi7naO1UtSmW4Cp-1H0ArvJD00WPmaFykJhya0jgVSC04iTw@mail.gmail.com>
References: <CAAzi7nZ_J_qDRc_jjtpZ2Xo5bTNd8pMgwzn0iP5VNsvp91ybOA@mail.gmail.com>
 <CAAzi7naO1UtSmW4Cp-1H0ArvJD00WPmaFykJhya0jgVSC04iTw@mail.gmail.com>
Message-ID: <CAAzi7nYKtYFdfZX1BN4HRoEYzZPEY-CGKGGh2zJHkSgBP5w=cA@mail.gmail.com>

Sorry, posted message in portuguese.
I would also like to know if anyone has plans to port AntiSmash
<http://antismash.secondarymetabolites.org/download.html>

On Mon, Oct 5, 2015 at 3:59 PM, Carlos Morais <morais at iq.usp.br> wrote:

> E quanto ao AntiSmash
> <http://antismash.secondarymetabolites.org/download.html>?
>
> On Mon, Oct 5, 2015 at 2:25 PM, Carlos Morais <morais at iq.usp.br> wrote:
>
>> Hi,
>>
>>     Is in anyone plans to make CheckM
>> <https://ecogenomics.github.io/CheckM/> available on BioLinux?
>>
>> Regards,
>>     Carlos
>>
>
>
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From l.lehtovirta at abdn.ac.uk  Tue Oct  6 11:30:16 2015
From: l.lehtovirta at abdn.ac.uk (Lehtovirta, Laura Elina)
Date: Tue, 6 Oct 2015 15:30:16 +0000
Subject: [Bio-Linux] Problems with MySQL local infile
Message-ID: <AM3PR04MB15086A16B1FF085733E9FCD9AF370@AM3PR04MB1508.eurprd04.prod.outlook.com>

Hi,



I'm having a problem with loading data into MySQL using LOAD DATA LOCAL INFILE. The error I'm getting is "The used command is not allowed with this MySQL version". I've tried "--local-infile" when starting MySQL and modified the my.cnf file to contain "local-infile=1".

Command "SHOW GLOBAL VARIABLES LIKE 'local_infile';" shows that local infile is on but does not get rid of the error. I'm using MySQL version 14.14 Distrib 5.5.44, for debian-linux-gnu (x86_64) using readline 6.3. Does anyone have suggestions how to fix this?



Many thanks in advance,



Laura

Dr Laura Lehtovirta-Morley
Postdoctoral Research Associate
Institute of Biological and Environmental Sciences
Cruickshank Building
University of Aberdeen
St Machar Drive
Aberdeen
AB24 3UU



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.
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From tbooth at ceh.ac.uk  Wed Oct  7 12:03:33 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 07 Oct 2015 17:03:33 +0100
Subject: [Bio-Linux] Problems with MySQL local infile
In-Reply-To: <AM3PR04MB15086A16B1FF085733E9FCD9AF370@AM3PR04MB1508.eurprd04.prod.outlook.com>
References: <AM3PR04MB15086A16B1FF085733E9FCD9AF370@AM3PR04MB1508.eurprd04.prod.outlook.com>
Message-ID: <1444233813.6624.190.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Laura,

Please ensure you join the mailing list to see all replies and so your
future postings won't be held up for moderation.

I believe the same question is answered here:
http://stackoverflow.com/questions/10762239/mysql-enable-load-data-local-infile

The key point is that because this feature is considered very insecure
it needs to be enabled on both the server and on the client.  It looks
like you have not enabled it on the server, which requires you to
edit /etc/mysql/my.cnf and to restart the server process (sudo restart
mysql).

A simpler option would be to copy the data over to the server (via SCP
if it is on a different machine, or else just ensure the file is
readable by the server process) and then do the import without the LOCAL
keyword.  Maybe this would be simper?

Cheers,

TIM

On Tue, 2015-10-06 at 15:30 +0000, Lehtovirta, Laura Elina wrote:
> Hi,
>  
> I'm having a problem with loading data into MySQL using LOAD DATA
> LOCAL INFILE. The error I'm getting is "The used command is not
> allowed with this MySQL version". I?ve tried ?--local-infile? when
> starting MySQL and modified the my.cnf file to contain
> ?local-infile=1?. 
> Command ?SHOW GLOBAL VARIABLES LIKE 'local_infile';? shows that local
> infile is on but does not get rid of the error. I?m using MySQL
> version 14.14 Distrib 5.5.44, for debian-linux-gnu (x86_64) using
> readline 6.3. Does anyone have suggestions how to fix this?
>  
> Many thanks in advance,
>  
> Laura
> 
>  
> 
> Dr Laura Lehtovirta-Morley
> 
> Postdoctoral Research Associate
> 
> Institute of Biological and Environmental Sciences
> 
> Cruickshank Building
> 
> University of Aberdeen
> 
> St Machar Drive
> 
> Aberdeen
> 
> AB24 3UU
> 
>  
> 
> 
> 
> 
> 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 <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  Wed Oct  7 12:34:41 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 07 Oct 2015 17:34:41 +0100
Subject: [Bio-Linux] CheckM
In-Reply-To: <CAAzi7nYKtYFdfZX1BN4HRoEYzZPEY-CGKGGh2zJHkSgBP5w=cA@mail.gmail.com>
References: <CAAzi7nZ_J_qDRc_jjtpZ2Xo5bTNd8pMgwzn0iP5VNsvp91ybOA@mail.gmail.com>
 <CAAzi7naO1UtSmW4Cp-1H0ArvJD00WPmaFykJhya0jgVSC04iTw@mail.gmail.com>
 <CAAzi7nYKtYFdfZX1BN4HRoEYzZPEY-CGKGGh2zJHkSgBP5w=cA@mail.gmail.com>
Message-ID: <1444235681.6624.212.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Carlos,

I don't speak Portuguese but I could guess what you meant. :-)

Regrettably I'm not promising any new packages at the moment because I'm
behind with updating the ones we have.  For AntiSmash I'd suggest
running the Debian installer script and see what happens.  It might
work, and if not post the error to this list.  Even if I did package it
you'd need to fetch the databases before it could be used.

CheckM looks simple enough but it needs pplacer which is already on my
TODO list but not started yet.  Again I (or others on the list) can try
to help if you have problems installing manually but I can't promise new
packages any time soon.

Cheers,

TIM

On Mon, 2015-10-05 at 16:00 -0300, Carlos Morais wrote:
> Sorry, posted message in portuguese.
> 
> I would also like to know if anyone has plans to port AntiSmash
> 
> On Mon, Oct 5, 2015 at 3:59 PM, Carlos Morais <morais at iq.usp.br>
> wrote:
>         E quanto ao AntiSmash?
>         
>         
>         On Mon, Oct 5, 2015 at 2:25 PM, Carlos Morais
>         <morais at iq.usp.br> wrote:
>                 Hi,
>                 
>                     Is in anyone plans to make CheckM available on
>                 BioLinux?
>                 
>                 
>                 Regards,
>                 
>                     Carlos
>                 
>         
>         
> 
> 
> _______________________________________________
> 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 ramendra.sarma at gmail.com  Mon Oct 12 06:48:31 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Mon, 12 Oct 2015 16:18:31 +0530
Subject: [Bio-Linux] X2Go Client behavoiur
Message-ID: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>

The X2goClient connects and disconnect immediately in my bio linux machine
during connection to a local bio linux server.The version is X2Go Client v.
4.0.5.0 (Qt - 4.8.6).

But I can ssh perfectly with the same machine. Why?

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






*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 sgrannem at staffmail.ed.ac.uk  Mon Oct 12 06:50:34 2015
From: sgrannem at staffmail.ed.ac.uk (Sander Granneman)
Date: Mon, 12 Oct 2015 11:50:34 +0100
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
References: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
Message-ID: <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>

We have had the same problem on a number of machines with x2go server.
The only thing that seems to be working reasonably well is to use LXDE as the default desktop.

Sander

> On Oct 12, 2015, at 11:48 AM, Ramendra Sarma <ramendra.sarma at gmail.com> wrote:
> 
> The X2goClient connects and disconnect immediately in my bio linux machine during connection to a local bio linux server.The version is X2Go Client v. 4.0.5.0 (Qt - 4.8.6).
> 
> But I can ssh perfectly with the same machine. Why?
> 
> -- 
> ----------------------------------------------------------------------------------------------------------------------------------------
> Dr R N Sarma
> Professor
> Department of Plant Breeding and Genetics
> Assam Agricultural University
> Jorhat-785013
> Assam, India
> web: www.aau.ac.in; <http://www.aaau.ac.in/> Phone: +91-376-2310526; +91-376231133(R); 9435350529(M)
> --------------------------------------------------------------------------------------------------------------------------
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

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

Sander Granneman, PhD
Wellcome Trust RCD Fellow
University of Edinburgh
Institute of Structural and Molecular Biology
Centre for Synthetic and Systems Biology (SynthSys)
University of Edinburgh
Max Born Crescent                                                                 
CH Waddington Building, room 3.06
EH9 3BF
Edinburgh

Phone:
office: +44 (0) 131 651 9082
lab: +44 (0) 131 651 9055

sgrannem at staffmail.ed.ac.uk

http://sandergranneman.bio.ed.ac.uk
http://www.csbe.ed.ac.uk/
------------------------------------------------------------------

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From Sejal.Modha at glasgow.ac.uk  Mon Oct 12 06:53:11 2015
From: Sejal.Modha at glasgow.ac.uk (Sejal Modha)
Date: Mon, 12 Oct 2015 10:53:11 +0000
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>
References: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
 <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>
Message-ID: <1444647379.3718.0.camel@modh01s-OptiPlex-790>

We had the same problem but it's fixed with MATE as default desktop as mentioned on the BL8 Wbsite.

On Mon, 2015-10-12 at 11:50 +0100, Sander Granneman wrote:
We have had the same problem on a number of machines with x2go server.
The only thing that seems to be working reasonably well is to use LXDE as the default desktop.


Sander

On Oct 12, 2015, at 11:48 AM, Ramendra Sarma <ramendra.sarma at gmail.com<mailto:ramendra.sarma at gmail.com>> wrote:

The X2goClient connects and disconnect immediately in my bio linux machine during connection to a local bio linux server.The version is X2Go Client v. 4.0.5.0 (Qt - 4.8.6).


But I can ssh perfectly with the same machine. Why?


--
----------------------------------------------------------------------------------------------------------------------------------------
Dr R N Sarma
Professor
Department of Plant Breeding and Genetics
Assam Agricultural University
Jorhat-785013
Assam, India
web: www.aau.ac.in;<http://www.aaau.ac.in/> Phone: +91-376-2310526; +91-376231133(R); 9435350529(M)
--------------------------------------------------------------------------------------------------------------------------

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


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

Sander Granneman, PhD
Wellcome Trust RCD Fellow
University of Edinburgh
Institute of Structural and Molecular Biology
Centre for Synthetic and Systems Biology (SynthSys)
University of Edinburgh
Max Born Crescent
CH Waddington Building, room 3.06
EH9 3BF
Edinburgh

Phone:
office: +44 (0) 131 651 9082
lab: +44 (0) 131 651 9055

sgrannem at staffmail.ed.ac.uk<mailto:sgrannem at staffmail.ed.ac.uk>

http://sandergranneman.bio.ed.ac.uk
http://www.csbe.ed.ac.uk/
------------------------------------------------------------------




The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


--
Sejal Modha

Bioinformatician
MRC-University of Glasgow Centre for Virus Research
117 Sir Michael Stoker Building
464 Bearsden Road
Glasgow
G61 1QH
Tel: 0141-330-4019
http://bioinformatics.cvr.ac.uk
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From ramendra.sarma at gmail.com  Mon Oct 12 06:59:26 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Mon, 12 Oct 2015 16:29:26 +0530
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <1444647379.3718.0.camel@modh01s-OptiPlex-790>
References: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
 <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>
 <1444647379.3718.0.camel@modh01s-OptiPlex-790>
Message-ID: <CAP3xa20cnaaoeqrC3Nh4GqDGJSbf2Xpa1hLqfk01YKJ3zPXN9g@mail.gmail.com>

I am using MATE as default desktop.

On 12 October 2015 at 16:23, Sejal Modha <Sejal.Modha at glasgow.ac.uk> wrote:

> We had the same problem but it's fixed with MATE as default desktop as
> mentioned on the BL8 Wbsite.
>
>
> On Mon, 2015-10-12 at 11:50 +0100, Sander Granneman wrote:
>
> We have had the same problem on a number of machines with x2go server.
>
> The only thing that seems to be working reasonably well is to use LXDE as
> the default desktop.
>
>
>
> Sander
>
>
> On Oct 12, 2015, at 11:48 AM, Ramendra Sarma <ramendra.sarma at gmail.com>
> wrote:
>
>
> The X2goClient connects and disconnect immediately in my bio linux machine
> during connection to a local bio linux server.The version is X2Go Client v.
> 4.0.5.0 (Qt - 4.8.6).
>
>
> But I can ssh perfectly with the same machine. Why?
>
>
> --
>
>
> ----------------------------------------------------------------------------------------------------------------------------------------
> *Dr R N Sarma*
> *Professor*
> *Department of Plant Breeding and Genetics*
> *Assam Agricultural University*
> *Jorhat-785013*
> *Assam, India*
> *web: www.aau.ac.in; <http://www.aaau.ac.in/> Phone: +91-376-2310526;
> +91-376231133(R); 9435350529(M)*
>
> --------------------------------------------------------------------------------------------------------------------------
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------------------------------------------
>
> Sander Granneman, PhD
> Wellcome Trust RCD Fellow
> University of Edinburgh
> Institute of Structural and Molecular Biology
> Centre for Synthetic and Systems Biology (SynthSys)
> University of Edinburgh
> Max Born Crescent
>
> CH Waddington Building, room 3.06
> EH9 3BF
> Edinburgh
>
> Phone:
> office: +44 (0) 131 651 9082
> lab: +44 (0) 131 651 9055
>
> sgrannem at staffmail.ed.ac.uk
>
> http://sandergranneman.bio.ed.ac.uk
> http://www.csbe.ed.ac.uk/
> ------------------------------------------------------------------
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> _______________________________________________
> Bio-Linux mailing listBio-Linux at nebclists.nerc.ac.ukhttp://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> --
> *Sejal Modha*
>
> Bioinformatician
> MRC-University of Glasgow Centre for Virus Research
> 117 Sir Michael Stoker Building
> 464 Bearsden Road
> Glasgow
> G61 1QH
> Tel: 0141-330-4019
> http://bioinformatics.cvr.ac.uk
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>


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






*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  Mon Oct 12 07:24:30 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Mon, 12 Oct 2015 12:24:30 +0100
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
References: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
Message-ID: <561B986E.2080109@minke-informatics.co.uk>

On 12/10/15 11:48, Ramendra Sarma wrote:
> The X2goClient connects and disconnect immediately in my bio linux
> machine during connection to a local bio linux server.The version isX2Go
> Client v. 4.0.5.0 (Qt - 4.8.6).
> 
> But I can ssh perfectly with the same machine. Why?

Hi, Ramen.

There is an incompatibility between the Windows "x2go" client and the
Linux "x2go" ckient that causes problems if you start a session under
the windows client, disconnect, then try to resume under the Linux client.

In this situation, you can either resume under the Windows client or ssh
into the server and kill the session from the command-line with:

  x2golistsessions_root
  x2goterminate-session xxxxxxxxxxxx

Where "xxxxxxxxxxxx" is the session that does not resume.

If this is NOT the problem, make sure you have selected the MATE desktop
session (the default is KDE, which is not supported in Bio-Linux).

If you contact me off-list with details of the server that is giving
problems I can check it out for you.

HTH,

  Tony.

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



From tony.travis at minke-informatics.co.uk  Mon Oct 12 07:26:23 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Mon, 12 Oct 2015 12:26:23 +0100
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>
References: <CAP3xa220HptEaf4_Ucowc2P6i5ZBQbhWXhBHg88EBBY_YS5--Q@mail.gmail.com>
 <00FA03AB-E285-4F24-8BE5-C4CA44B20116@staffmail.ed.ac.uk>
Message-ID: <561B98DF.3020507@minke-informatics.co.uk>

On 12/10/15 11:50, Sander Granneman wrote:
> We have had the same problem on a number of machines with x2go server.
> The only thing that seems to be working reasonably well is to use LXDE
> as the default desktop.

Hi, Sander.

I think some of your servers are still running Bio-Linux 7 and need to
be upgraded. Let me know off-list if you would like me to investigate?

Bye,

  Tony.

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


From ramen5in at yahoo.co.in  Mon Oct 12 07:52:41 2015
From: ramen5in at yahoo.co.in (Dr. R. N. Sarma)
Date: Mon, 12 Oct 2015 19:52:41 +0800
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <561B986E.2080109@minke-informatics.co.uk>
Message-ID: <1444650761.21837.YahooMailAndroidMobile@web193005.mail.sg3.yahoo.com>

it is with my linux to connect aryabhatta.

Sent from Yahoo Mail on Android

From:"Tony Travis" <tony.travis at minke-informatics.co.uk>
Date:Mon, 12 Oct, 2015 at 4:54 PM
Subject:Re: [Bio-Linux] X2Go Client behavoiur

On 12/10/15 11:48, Ramendra Sarma wrote:
> The X2goClient connects and disconnect immediately in my bio linux
> machine during connection to a local bio linux server.The version isX2Go
> Client v. 4.0.5.0 (Qt - 4.8.6).
> 
> But I can ssh perfectly with the same machine. Why?

Hi, Ramen.

There is an incompatibility between the Windows "x2go" client and the
Linux "x2go" ckient that causes problems if you start a session under
the windows client, disconnect, then try to resume under the Linux client.

In this situation, you can either resume under the Windows client or ssh
into the server and kill the session from the command-line with:

? x2golistsessions_root
? x2goterminate-session xxxxxxxxxxxx

Where "xxxxxxxxxxxx" is the session that does not resume.

If this is NOT the problem, make sure you have selected the MATE desktop
session (the default is KDE, which is not supported in Bio-Linux).

If you contact me off-list with details of the server that is giving
problems I can check it out for you.

HTH,

? Tony.

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



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

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From tony.travis at abdn.ac.uk  Tue Oct 13 05:17:26 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 13 Oct 2015 10:17:26 +0100
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <1444650761.21837.YahooMailAndroidMobile@web193005.mail.sg3.yahoo.com>
References: <1444650761.21837.YahooMailAndroidMobile@web193005.mail.sg3.yahoo.com>
Message-ID: <561CCC26.4020302@abdn.ac.uk>

On 12/10/15 12:52, Dr. R. N. Sarma wrote:
> it is with my linux to connect aryabhatta.

Hi, Ramen.

I've checked "aryabhatta". The problem is nothing to do with Bio-Linux.
It is caused by "virtualenvwrapper". I've disabled it so that you can
try "x2go":

> root at Aryabhatta:/etc/profile.d# mv -i virtualenvwrapper.sh
> virtualenvwrapper.sh.disable

[Please contact the person who installed it to enable
"virtualenvwrapper" again]

HTH,

  Tony.

> Sent from Yahoo Mail on Android
> <https://overview.mail.yahoo.com/mobile/?.src=Android>
>
> ------------------------------------------------------------------------
> *From*:"Tony Travis" <tony.travis at minke-informatics.co.uk>
> *Date*:Mon, 12 Oct, 2015 at 4:54 PM
> *Subject*:Re: [Bio-Linux] X2Go Client behavoiur
>
> On 12/10/15 11:48, Ramendra Sarma wrote:
>> The X2goClient connects and disconnect immediately in my bio linux
>> machine during connection to a local bio linux server.The version isX2Go
>> Client v. 4.0.5.0 (Qt - 4.8.6).
>>
>> But I can ssh perfectly with the same machine. Why?
>
> Hi, Ramen.
>
> There is an incompatibility between the Windows "x2go" client and the
> Linux "x2go" ckient that causes problems if you start a session under
> the windows client, disconnect, then try to resume under the Linux client.
>
> In this situation, you can either resume under the Windows client or ssh
> into the server and kill the session from the command-line with:
>
>   x2golistsessions_root
>   x2goterminate-session xxxxxxxxxxxx
>
> Where "xxxxxxxxxxxx" is the session that does not resume.
>
> If this is NOT the problem, make sure you have selected the MATE desktop
> session (the default is KDE, which is not supported in Bio-Linux).
>
> If you contact me off-list with details of the server that is giving
> problems I can check it out for you.
>
> 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
> <javascript:return>
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk <javascript:return>
> 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
>


--
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 ramendra.sarma at gmail.com  Tue Oct 13 05:46:10 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Tue, 13 Oct 2015 15:16:10 +0530
Subject: [Bio-Linux] X2Go Client behavoiur
In-Reply-To: <561CCC26.4020302@abdn.ac.uk>
References: <1444650761.21837.YahooMailAndroidMobile@web193005.mail.sg3.yahoo.com>
 <561CCC26.4020302@abdn.ac.uk>
Message-ID: <CAP3xa215uhhEOsFNZSxOs=SuMWhuDxyvkFO_otniL5JzUuqhqA@mail.gmail.com>

Hi Tony,
Thank you for rectifying the fault for use X2go client.

Hi, Ramen.

I've checked "aryabhatta". The problem is nothing to do with Bio-Linux.
It is caused by "virtualenvwrapper". I've disabled it so that you can
try "x2go":

> root at Aryabhatta:/etc/profile.d# mv -i virtualenvwrapper.sh
> virtualenvwrapper.sh.disable

[Please contact the person who installed it to enable
"virtualenvwrapper" again]

On 13 October 2015 at 14:47, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 12/10/15 12:52, Dr. R. N. Sarma wrote:
> > it is with my linux to connect aryabhatta.
>
> Hi, Ramen.
>
> I've checked "aryabhatta". The problem is nothing to do with Bio-Linux.
> It is caused by "virtualenvwrapper". I've disabled it so that you can
> try "x2go":
>
> > root at Aryabhatta:/etc/profile.d# mv -i virtualenvwrapper.sh
> > virtualenvwrapper.sh.disable
>
> [Please contact the person who installed it to enable
> "virtualenvwrapper" again]
>
> HTH,
>
>   Tony.
>
> > Sent from Yahoo Mail on Android
> > <https://overview.mail.yahoo.com/mobile/?.src=Android>
> >
> > ------------------------------------------------------------------------
> > *From*:"Tony Travis" <tony.travis at minke-informatics.co.uk>
> > *Date*:Mon, 12 Oct, 2015 at 4:54 PM
> > *Subject*:Re: [Bio-Linux] X2Go Client behavoiur
> >
> > On 12/10/15 11:48, Ramendra Sarma wrote:
> >> The X2goClient connects and disconnect immediately in my bio linux
> >> machine during connection to a local bio linux server.The version isX2Go
> >> Client v. 4.0.5.0 (Qt - 4.8.6).
> >>
> >> But I can ssh perfectly with the same machine. Why?
> >
> > Hi, Ramen.
> >
> > There is an incompatibility between the Windows "x2go" client and the
> > Linux "x2go" ckient that causes problems if you start a session under
> > the windows client, disconnect, then try to resume under the Linux
> client.
> >
> > In this situation, you can either resume under the Windows client or ssh
> > into the server and kill the session from the command-line with:
> >
> >   x2golistsessions_root
> >   x2goterminate-session xxxxxxxxxxxx
> >
> > Where "xxxxxxxxxxxx" is the session that does not resume.
> >
> > If this is NOT the problem, make sure you have selected the MATE desktop
> > session (the default is KDE, which is not supported in Bio-Linux).
> >
> > If you contact me off-list with details of the server that is giving
> > problems I can check it out for you.
> >
> > 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
> > <javascript:return>
> >
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk <javascript:return>
> > 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
> >
>
>
> --
> 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
>



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






*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 morais at iq.usp.br  Thu Oct 15 11:28:32 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Thu, 15 Oct 2015 12:28:32 -0300
Subject: [Bio-Linux] Trinity added, Mothur and Mira updated
In-Reply-To: <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
Message-ID: <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>

Thanks a lot for the update.

However, it is trying to compile Jellyfish on the go. I'm attaching the
output. Relevant part:

Trinity version: v2.0.6
...
-------------------------------------------
----------- Jellyfish  --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------

Wednesday, October 14, 2015: 13:46:18   CMD: /usr/bin/jellyfish count -t 15
-m 25 -s 14446126223  --canonical  both.fa
mkdir: cannot create directory ?/usr/bin/.libs?: Permission denied
/usr/bin/jellyfish: line 202: cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3:
No such file or directory
g++: error: sub_commands/jellyfish.o: No such file or directory
g++: error: sub_commands/count_main.o: No such file or directory
g++: error: sub_commands/info_main.o: No such file or directory
g++: error: sub_commands/dump_main.o: No such file or directory
g++: error: sub_commands/histo_main.o: No such file or directory
g++: error: sub_commands/stats_main.o: No such file or directory
g++: error: sub_commands/merge_main.o: No such file or directory
g++: error: sub_commands/bc_main.o: No such file or directory
g++: error: sub_commands/query_main.o: No such file or directory
g++: error: sub_commands/cite_main.o: No such file or directory
g++: error: sub_commands/mem_main.o: No such file or directory
g++: error: jellyfish/merge_files.o: No such file or directory
g++: error: ./.libs/libjellyfish-2.0.so: No such file or directorynError,
cmd: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223  --canonical
both.fa died with ret 256 at /usr/lib/trinityrnaseq/Trinity line 2115.

Trinity run failed. Must investigate error above.

On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran <kirannbishwa01 at gmail.com>
wrote:

> Thanks for the update !
>
> On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>
>> Hi All,
>>
>> I've been doing a round of package updates on Bio-Linux 8 over the last
>> week.  We now have both Mothur and Mira updated to the latest versions:
>>
>> mira-assembler package is version 4.9.5
>> mothur package is version 1.36.1
>>
>> Both will be updated by the package updater. If you experience any
>> problems or regressions with these new packages please let me know.
>>
>> I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
>> been added to the package repository (http://trinityrnaseq.github.io/).
>> Various modifications have been made to Trinity to make it integrate
>> nicely with the other packages on the system, so if you have problems
>> running it please let me know and I'll check if it is maybe something
>> that got messed up in the packaging.
>>
>> trinityrnaseq package is version 2.0.6
>>
>> To get it: sudo apt-get install trinityrnaseq
>> then just type: "Trinity" (with the capital T)
>>
>> The credit for all this goes mainly to Michael and Andreas from the
>> Debian Med project who maintain these packages in Debian.  I've been
>> able to take what they made and backport it to Bio-Linux for you.
>>
>> Cheers,
>>
>> 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
>>
>
>
>
> --
> - Bish
>
>
>
> _______________________________________________
> 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  Sat Oct 17 11:37:44 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Sat, 17 Oct 2015 21:07:44 +0530
Subject: [Bio-Linux] Fwd: problem in loading biolinux8
Message-ID: <CAP3xa21mh6qkzNA6QPjmT8B8ePvXfXghuw=EGuFAT6mN2UNC_w@mail.gmail.com>

Hi,
Biolinux 8 which was working 2 days back in my HP notebook for last one
year is not loading. I get some chracters in screen,which I overcomed by
esc key for 2 months. But from today, after putting my correct p/w also the
screen does not show final linux window. But revert back to p/w screen.
What should I do now?
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From tony.travis at minke-informatics.co.uk  Sun Oct 18 18:25:50 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Sun, 18 Oct 2015 23:25:50 +0100
Subject: [Bio-Linux] Fwd: problem in loading biolinux8
In-Reply-To: <CAP3xa21mh6qkzNA6QPjmT8B8ePvXfXghuw=EGuFAT6mN2UNC_w@mail.gmail.com>
References: <CAP3xa21mh6qkzNA6QPjmT8B8ePvXfXghuw=EGuFAT6mN2UNC_w@mail.gmail.com>
Message-ID: <56241C6E.9040300@minke-informatics.co.uk>

On 17/10/15 16:37, Ramendra Sarma wrote:
> Hi,
> Biolinux 8 which was working 2 days back in my HP notebook for last one
> year is not loading. I get some chracters in screen,which I overcomed by
> esc key for 2 months. But from today, after putting my correct p/w also
> the screen does not show final linux window. But revert back to p/w
> screen.  What should I do now?

Hi, Ramen.

First thing is to make sure there is not a key stuck down on your
keyboard: Switch your laptop off, turn it upside down and bang all the
keys to see if anything falls out. Quite often, keys get stuck down and
then auto-repeat. It's possible that one of the [F]unction keys is
sticking, and pressing "Esc" along the top row might very well release it.

If that is not the problem, boot your laptop from a Bio-Linux USB-stick.
If you get the same symptoms, then it's likely to be a hardware fault on
your laptop: Keyboards are readily available for most types of laptop
and are not difficult to fit. However, you do need to find out how to
fit them on your particular laptop without breaking any parts.

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 ramen5in at yahoo.co.in  Sun Oct 18 20:59:13 2015
From: ramen5in at yahoo.co.in (Dr. R. N. Sarma)
Date: Mon, 19 Oct 2015 08:59:13 +0800
Subject: [Bio-Linux] Fwd: problem in loading biolinux8
In-Reply-To: <56241C6E.9040300@minke-informatics.co.uk>
Message-ID: <1445216353.38142.YahooMailAndroidMobile@web193002.mail.sg3.yahoo.com>

Thank you, Tony. I shall try.

Sent from Yahoo Mail on Android

From:"Tony Travis" <tony.travis at minke-informatics.co.uk>
Date:Mon, 19 Oct, 2015 at 3:56 AM
Subject:Re: [Bio-Linux] Fwd: problem in loading biolinux8

On 17/10/15 16:37, Ramendra Sarma wrote:
> Hi,
> Biolinux 8 which was working 2 days back in my HP notebook for last one
> year is not loading. I get some chracters in screen,which I overcomed by
> esc key for 2 months. But from today, after putting my correct p/w also
> the screen does not show final linux window. But revert back to p/w
> screen.? What should I do now?

Hi, Ramen.

First thing is to make sure there is not a key stuck down on your
keyboard: Switch your laptop off, turn it upside down and bang all the
keys to see if anything falls out. Quite often, keys get stuck down and
then auto-repeat. It's possible that one of the [F]unction keys is
sticking, and pressing "Esc" along the top row might very well release it.

If that is not the problem, boot your laptop from a Bio-Linux USB-stick.
If you get the same symptoms, then it's likely to be a hardware fault on
your laptop: Keyboards are readily available for most types of laptop
and are not difficult to fit. However, you do need to find out how to
fit them on your particular laptop without breaking any parts.

HTH,

? Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk
mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk
_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

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From tbooth at ceh.ac.uk  Mon Oct 19 07:14:53 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 19 Oct 2015 12:14:53 +0100
Subject: [Bio-Linux] Expired key warning when updating packages
Message-ID: <1445253293.3511.14.camel@wllt1771.nerc-wallingford.ac.uk>

Hi All,

You might see an error today about an expired signing key when updating
packages on the system.  This only pertains to the R core updates and
the error should resolve itself after you upgrade to the latest version
of the "bio-linux-keyring" package, to which I have just added an
updated key file.  So in other words, there is nothing to worry about.

Best,

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 ramendra.sarma at gmail.com  Mon Oct 26 01:00:43 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Mon, 26 Oct 2015 10:30:43 +0530
Subject: [Bio-Linux] Biolinux screen is missing
Message-ID: <CAP3xa20LqaiLWWdfQruTZe_y4Qs1NdRgCOf=xzkRkFH2bYV41g@mail.gmail.com>

Hi,
I want to use my Bio Linux 8 desktop back ground which I lost somehow. In
'System Settings / Appearance / Wallpapers / ", the use of path "
/var/spool/BL_auto_cycling_background.jpg" is not helping. The commnand ~$
dpkg -L bio-linux-themes-v8  returns with the message "Package
`bio-linux-themes-v8' does not contain any files (!)".
How to resolve the issue?

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






*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  Mon Oct 26 06:07:08 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Mon, 26 Oct 2015 10:07:08 +0000
Subject: [Bio-Linux] Biolinux screen is missing
In-Reply-To: <CAP3xa20LqaiLWWdfQruTZe_y4Qs1NdRgCOf=xzkRkFH2bYV41g@mail.gmail.com>
References: <CAP3xa20LqaiLWWdfQruTZe_y4Qs1NdRgCOf=xzkRkFH2bYV41g@mail.gmail.com>
Message-ID: <562DFB4C.40504@minke-informatics.co.uk>

On 26/10/15 05:00, Ramendra Sarma wrote:
> Hi,
> I want to use my Bio Linux 8 desktop back ground which I lost somehow.
> In 'System Settings / Appearance / Wallpapers / ", the use of path " 
> /var/spool/BL_auto_cycling_background.jpg" is not helping. The commnand
> ~$ dpkg -L bio-linux-themes-v8  returns with the message "Package
> `bio-linux-themes-v8' does not contain any files (!)".
> How to resolve the issue?

Hi, Ramen.

Check that the package is installed and you are not just looking at the
entry for remaining configuration files left after removing it (or it
being removed automatically). It should look something like this:

> ajt at beluga:~$ dpkg -l bio-linux-themes-v8
> Desired=Unknown/Install/Remove/Purge/Hold
> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name                        Version            Architecture       Description
> +++-===========================-==================-==================-===========================================================
> ii  bio-linux-themes-v8         8.0-22             all                Graphics, icons, wallpaper and desktop settings for Bio-Lin

If it says "rc" instead of "ii", then the package was removed leaving
its configuration files still installed (i.e. not 'purged').

The files contained in the package are:

> ajt at beluga:~$ dpkg -L bio-linux-themes-v8
> /.
> /usr
> /usr/share
> /usr/share/gdm
> /usr/share/gdm/themes
> /usr/share/gdm/themes/bio-linux5
> /usr/share/gdm/themes/bio-linux5/screenshot.png
> /usr/share/gdm/themes/bio-linux5/GdmGreeterTheme.desktop
> /usr/share/gdm/themes/bio-linux5/quit.png
> /usr/share/gdm/themes/bio-linux5/dna-1400x1250.jpg
> /usr/share/gdm/themes/bio-linux5/options.png
> /usr/share/gdm/themes/bio-linux5/language.png
> /usr/share/gdm/themes/bio-linux5/bio-linux5.xml
> /usr/share/gdm/themes/bio-linux5/nebc.png
> /usr/share/gdm/themes/bio-linux5/nerc.png
> /usr/share/gdm/themes/bio-linux5/system.png
> /usr/share/gdm/themes/bio-linux5/session.png
> /usr/share/gdm/themes/bio-linux5/nebclogo.png
> /usr/share/glib-2.0
> /usr/share/glib-2.0/schemas
> /usr/share/glib-2.0/schemas/mate-bl.gschema.override
> /usr/share/glib-2.0/schemas/zz-bio-linux.gschema.override
> /usr/share/doc
> /usr/share/doc/bio-linux-themes-v8
> /usr/share/doc/bio-linux-themes-v8/README.Bio-Linux
> /usr/share/doc/bio-linux-themes-v8/credits.txt
> /usr/share/bio-linux-icons
> /usr/share/bio-linux-icons/nebc_piclogo_bl.png
> /usr/share/bio-linux-icons/nebc_piclogo.png
> /usr/share/gconf
> /usr/share/gconf/defaults
> /usr/share/gconf/defaults/95_bio-linux-settings.entries
> /usr/share/backgrounds
> /usr/share/backgrounds/BL_Butterfly_by_Tony_Travis.jpg
> /usr/share/backgrounds/BL_Lycaena_tityrus_by_Bas_van_Schooten.jpg
> /usr/share/backgrounds/BL_Jellyfish_by_Tony_Travis.jpg
> /usr/share/backgrounds/BL_Bat_by_Bas_van_Schooten.jpg
> /usr/share/backgrounds/BL_Bee_by_Stefan_Buzoianu.jpg
> /usr/share/backgrounds/BL_Blossom_by_Itaru_Dekio.jpg
> /usr/share/backgrounds/Grasshopper_by_Marcin_Jankowski_BL_Logo.jpg
> /usr/share/backgrounds/BL_Berries_by_Sergui_Ponochevny.jpg
> /usr/share/backgrounds/BL_Penguin_Silhouette_by_Matthias_Zepper.jpg
> /usr/share/backgrounds/BL_Travertine_Encrustation_by_Katherine_Wright.jpg
> /usr/share/backgrounds/bio-linux-5.jpg
> /usr/share/backgrounds/BL_Golden_Grass_by_James_Mategko.jpg
> /usr/share/bio-linux-themes-v8
> /usr/share/bio-linux-themes-v8/bl_wallpaper_cycler.sh

Check to see if any of these files are still present.

If necessary, re-install the package:

  sudo apt-get --reinstall install bio-linux-themes-v8

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 dksamuel2 at gmail.com  Mon Oct 26 06:19:20 2015
From: dksamuel2 at gmail.com (Duleep Samuel)
Date: Mon, 26 Oct 2015 15:49:20 +0530
Subject: [Bio-Linux] Biolinux screen is missing
In-Reply-To: <562DFB4C.40504@minke-informatics.co.uk>
References: <CAP3xa20LqaiLWWdfQruTZe_y4Qs1NdRgCOf=xzkRkFH2bYV41g@mail.gmail.com>
 <562DFB4C.40504@minke-informatics.co.uk>
Message-ID: <CABqBg+DpupBtpy1Tg_Vf0ZyW4hN2st+SDb4fs7eQ8KuLkJhPPA@mail.gmail.com>

I suggest you reinstall, as I am not sure where the error would be, Samuel,
Bangalore

On Mon, Oct 26, 2015 at 3:37 PM, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 26/10/15 05:00, Ramendra Sarma wrote:
> > Hi,
> > I want to use my Bio Linux 8 desktop back ground which I lost somehow.
> > In 'System Settings / Appearance / Wallpapers / ", the use of path "
> > /var/spool/BL_auto_cycling_background.jpg" is not helping. The commnand
> > ~$ dpkg -L bio-linux-themes-v8  returns with the message "Package
> > `bio-linux-themes-v8' does not contain any files (!)".
> > How to resolve the issue?
>
> Hi, Ramen.
>
> Check that the package is installed and you are not just looking at the
> entry for remaining configuration files left after removing it (or it
> being removed automatically). It should look something like this:
>
> > ajt at beluga:~$ dpkg -l bio-linux-themes-v8
> > Desired=Unknown/Install/Remove/Purge/Hold
> > |
> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> > ||/ Name                        Version            Architecture
>  Description
> >
> +++-===========================-==================-==================-===========================================================
> > ii  bio-linux-themes-v8         8.0-22             all
> Graphics, icons, wallpaper and desktop settings for Bio-Lin
>
> If it says "rc" instead of "ii", then the package was removed leaving
> its configuration files still installed (i.e. not 'purged').
>
> The files contained in the package are:
>
> > ajt at beluga:~$ dpkg -L bio-linux-themes-v8
> > /.
> > /usr
> > /usr/share
> > /usr/share/gdm
> > /usr/share/gdm/themes
> > /usr/share/gdm/themes/bio-linux5
> > /usr/share/gdm/themes/bio-linux5/screenshot.png
> > /usr/share/gdm/themes/bio-linux5/GdmGreeterTheme.desktop
> > /usr/share/gdm/themes/bio-linux5/quit.png
> > /usr/share/gdm/themes/bio-linux5/dna-1400x1250.jpg
> > /usr/share/gdm/themes/bio-linux5/options.png
> > /usr/share/gdm/themes/bio-linux5/language.png
> > /usr/share/gdm/themes/bio-linux5/bio-linux5.xml
> > /usr/share/gdm/themes/bio-linux5/nebc.png
> > /usr/share/gdm/themes/bio-linux5/nerc.png
> > /usr/share/gdm/themes/bio-linux5/system.png
> > /usr/share/gdm/themes/bio-linux5/session.png
> > /usr/share/gdm/themes/bio-linux5/nebclogo.png
> > /usr/share/glib-2.0
> > /usr/share/glib-2.0/schemas
> > /usr/share/glib-2.0/schemas/mate-bl.gschema.override
> > /usr/share/glib-2.0/schemas/zz-bio-linux.gschema.override
> > /usr/share/doc
> > /usr/share/doc/bio-linux-themes-v8
> > /usr/share/doc/bio-linux-themes-v8/README.Bio-Linux
> > /usr/share/doc/bio-linux-themes-v8/credits.txt
> > /usr/share/bio-linux-icons
> > /usr/share/bio-linux-icons/nebc_piclogo_bl.png
> > /usr/share/bio-linux-icons/nebc_piclogo.png
> > /usr/share/gconf
> > /usr/share/gconf/defaults
> > /usr/share/gconf/defaults/95_bio-linux-settings.entries
> > /usr/share/backgrounds
> > /usr/share/backgrounds/BL_Butterfly_by_Tony_Travis.jpg
> > /usr/share/backgrounds/BL_Lycaena_tityrus_by_Bas_van_Schooten.jpg
> > /usr/share/backgrounds/BL_Jellyfish_by_Tony_Travis.jpg
> > /usr/share/backgrounds/BL_Bat_by_Bas_van_Schooten.jpg
> > /usr/share/backgrounds/BL_Bee_by_Stefan_Buzoianu.jpg
> > /usr/share/backgrounds/BL_Blossom_by_Itaru_Dekio.jpg
> > /usr/share/backgrounds/Grasshopper_by_Marcin_Jankowski_BL_Logo.jpg
> > /usr/share/backgrounds/BL_Berries_by_Sergui_Ponochevny.jpg
> > /usr/share/backgrounds/BL_Penguin_Silhouette_by_Matthias_Zepper.jpg
> > /usr/share/backgrounds/BL_Travertine_Encrustation_by_Katherine_Wright.jpg
> > /usr/share/backgrounds/bio-linux-5.jpg
> > /usr/share/backgrounds/BL_Golden_Grass_by_James_Mategko.jpg
> > /usr/share/bio-linux-themes-v8
> > /usr/share/bio-linux-themes-v8/bl_wallpaper_cycler.sh
>
> Check to see if any of these files are still present.
>
> If necessary, re-install the package:
>
>   sudo apt-get --reinstall install bio-linux-themes-v8
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux 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 Oct 27 00:25:10 2015
From: ramendra.sarma at gmail.com (Ramendra Sarma)
Date: Tue, 27 Oct 2015 09:55:10 +0530
Subject: [Bio-Linux] Biolinux screen is missing
In-Reply-To: <562DFB4C.40504@minke-informatics.co.uk>
References: <CAP3xa20LqaiLWWdfQruTZe_y4Qs1NdRgCOf=xzkRkFH2bYV41g@mail.gmail.com>
 <562DFB4C.40504@minke-informatics.co.uk>
Message-ID: <CAP3xa21LYM+w1CYxN=jATVY-280o51QKszLH6Y03xJd+4M5a1A@mail.gmail.com>

Hi Tony,
Thank you for your help. Bio linux background is back after re-installing
(sudo apt-get --reinstall install bio-linux-themes-v8
)  and changing the path in wallpaper using
/var/spool/BL_auto_cycling_background.jpg.

Ramen

On 26 October 2015 at 15:37, Tony Travis <
tony.travis at minke-informatics.co.uk> wrote:

> On 26/10/15 05:00, Ramendra Sarma wrote:
> > Hi,
> > I want to use my Bio Linux 8 desktop back ground which I lost somehow.
> > In 'System Settings / Appearance / Wallpapers / ", the use of path "
> > /var/spool/BL_auto_cycling_background.jpg" is not helping. The commnand
> > ~$ dpkg -L bio-linux-themes-v8  returns with the message "Package
> > `bio-linux-themes-v8' does not contain any files (!)".
> > How to resolve the issue?
>
> Hi, Ramen.
>
> Check that the package is installed and you are not just looking at the
> entry for remaining configuration files left after removing it (or it
> being removed automatically). It should look something like this:
>
> > ajt at beluga:~$ dpkg -l bio-linux-themes-v8
> > Desired=Unknown/Install/Remove/Purge/Hold
> > |
> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
> > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> > ||/ Name                        Version            Architecture
>  Description
> >
> +++-===========================-==================-==================-===========================================================
> > ii  bio-linux-themes-v8         8.0-22             all
> Graphics, icons, wallpaper and desktop settings for Bio-Lin
>
> If it says "rc" instead of "ii", then the package was removed leaving
> its configuration files still installed (i.e. not 'purged').
>
> The files contained in the package are:
>
> > ajt at beluga:~$ dpkg -L bio-linux-themes-v8
> > /.
> > /usr
> > /usr/share
> > /usr/share/gdm
> > /usr/share/gdm/themes
> > /usr/share/gdm/themes/bio-linux5
> > /usr/share/gdm/themes/bio-linux5/screenshot.png
> > /usr/share/gdm/themes/bio-linux5/GdmGreeterTheme.desktop
> > /usr/share/gdm/themes/bio-linux5/quit.png
> > /usr/share/gdm/themes/bio-linux5/dna-1400x1250.jpg
> > /usr/share/gdm/themes/bio-linux5/options.png
> > /usr/share/gdm/themes/bio-linux5/language.png
> > /usr/share/gdm/themes/bio-linux5/bio-linux5.xml
> > /usr/share/gdm/themes/bio-linux5/nebc.png
> > /usr/share/gdm/themes/bio-linux5/nerc.png
> > /usr/share/gdm/themes/bio-linux5/system.png
> > /usr/share/gdm/themes/bio-linux5/session.png
> > /usr/share/gdm/themes/bio-linux5/nebclogo.png
> > /usr/share/glib-2.0
> > /usr/share/glib-2.0/schemas
> > /usr/share/glib-2.0/schemas/mate-bl.gschema.override
> > /usr/share/glib-2.0/schemas/zz-bio-linux.gschema.override
> > /usr/share/doc
> > /usr/share/doc/bio-linux-themes-v8
> > /usr/share/doc/bio-linux-themes-v8/README.Bio-Linux
> > /usr/share/doc/bio-linux-themes-v8/credits.txt
> > /usr/share/bio-linux-icons
> > /usr/share/bio-linux-icons/nebc_piclogo_bl.png
> > /usr/share/bio-linux-icons/nebc_piclogo.png
> > /usr/share/gconf
> > /usr/share/gconf/defaults
> > /usr/share/gconf/defaults/95_bio-linux-settings.entries
> > /usr/share/backgrounds
> > /usr/share/backgrounds/BL_Butterfly_by_Tony_Travis.jpg
> > /usr/share/backgrounds/BL_Lycaena_tityrus_by_Bas_van_Schooten.jpg
> > /usr/share/backgrounds/BL_Jellyfish_by_Tony_Travis.jpg
> > /usr/share/backgrounds/BL_Bat_by_Bas_van_Schooten.jpg
> > /usr/share/backgrounds/BL_Bee_by_Stefan_Buzoianu.jpg
> > /usr/share/backgrounds/BL_Blossom_by_Itaru_Dekio.jpg
> > /usr/share/backgrounds/Grasshopper_by_Marcin_Jankowski_BL_Logo.jpg
> > /usr/share/backgrounds/BL_Berries_by_Sergui_Ponochevny.jpg
> > /usr/share/backgrounds/BL_Penguin_Silhouette_by_Matthias_Zepper.jpg
> > /usr/share/backgrounds/BL_Travertine_Encrustation_by_Katherine_Wright.jpg
> > /usr/share/backgrounds/bio-linux-5.jpg
> > /usr/share/backgrounds/BL_Golden_Grass_by_James_Mategko.jpg
> > /usr/share/bio-linux-themes-v8
> > /usr/share/bio-linux-themes-v8/bl_wallpaper_cycler.sh
>
> Check to see if any of these files are still present.
>
> If necessary, re-install the package:
>
>   sudo apt-get --reinstall install bio-linux-themes-v8
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



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






*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 carlos88morais at gmail.com  Mon Oct 26 06:41:35 2015
From: carlos88morais at gmail.com (Carlos Morais)
Date: Mon, 26 Oct 2015 08:41:35 -0200
Subject: [Bio-Linux] Trinity added, Mothur and Mira updated
In-Reply-To: <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
 <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
Message-ID: <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>

Anybody else experienced this error? Any ideas?
Thanks
Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br> escreveu:

> Thanks a lot for the update.
>
> However, it is trying to compile Jellyfish on the go. I'm attaching the
> output. Relevant part:
>
> Trinity version: v2.0.6
> ...
> -------------------------------------------
> ----------- Jellyfish  --------------------
> -- (building a k-mer catalog from reads) --
> -------------------------------------------
>
> Wednesday, October 14, 2015: 13:46:18   CMD: /usr/bin/jellyfish count -t
> 15 -m 25 -s 14446126223  --canonical  both.fa
> mkdir: cannot create directory ?/usr/bin/.libs?: Permission denied
> /usr/bin/jellyfish: line 202: cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3:
> No such file or directory
> g++: error: sub_commands/jellyfish.o: No such file or directory
> g++: error: sub_commands/count_main.o: No such file or directory
> g++: error: sub_commands/info_main.o: No such file or directory
> g++: error: sub_commands/dump_main.o: No such file or directory
> g++: error: sub_commands/histo_main.o: No such file or directory
> g++: error: sub_commands/stats_main.o: No such file or directory
> g++: error: sub_commands/merge_main.o: No such file or directory
> g++: error: sub_commands/bc_main.o: No such file or directory
> g++: error: sub_commands/query_main.o: No such file or directory
> g++: error: sub_commands/cite_main.o: No such file or directory
> g++: error: sub_commands/mem_main.o: No such file or directory
> g++: error: jellyfish/merge_files.o: No such file or directory
> g++: error: ./.libs/libjellyfish-2.0.so: No such file or directorynError,
> cmd: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223  --canonical
> both.fa died with ret 256 at /usr/lib/trinityrnaseq/Trinity line 2115.
>
> Trinity run failed. Must investigate error above.
>
> On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran <kirannbishwa01 at gmail.com>
> wrote:
>
>> Thanks for the update !
>>
>> On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>>
>>> Hi All,
>>>
>>> I've been doing a round of package updates on Bio-Linux 8 over the last
>>> week.  We now have both Mothur and Mira updated to the latest versions:
>>>
>>> mira-assembler package is version 4.9.5
>>> mothur package is version 1.36.1
>>>
>>> Both will be updated by the package updater. If you experience any
>>> problems or regressions with these new packages please let me know.
>>>
>>> I'm also pleased to say that the Trinity RNA-Seq De novo assembler has
>>> been added to the package repository (http://trinityrnaseq.github.io/).
>>> Various modifications have been made to Trinity to make it integrate
>>> nicely with the other packages on the system, so if you have problems
>>> running it please let me know and I'll check if it is maybe something
>>> that got messed up in the packaging.
>>>
>>> trinityrnaseq package is version 2.0.6
>>>
>>> To get it: sudo apt-get install trinityrnaseq
>>> then just type: "Trinity" (with the capital T)
>>>
>>> The credit for all this goes mainly to Michael and Andreas from the
>>> Debian Med project who maintain these packages in Debian.  I've been
>>> able to take what they made and backport it to Bio-Linux for you.
>>>
>>> Cheers,
>>>
>>> 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
>>>
>>
>>
>>
>> --
>> - Bish
>>
>>
>>
>> _______________________________________________
>> 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 tbooth at ceh.ac.uk  Tue Oct 27 13:31:19 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 27 Oct 2015 17:31:19 +0000
Subject: [Bio-Linux] Trinity added,
 Mothur and Mira updated - jellyfish problem
In-Reply-To: <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
 <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
 <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>
Message-ID: <1445967079.29689.31.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Carlos,

This looks to me like someone (maybe me) stuffed up the jellyfish
package and installed the wrong file into /usr/bin.  It seems to be a
simple typo in the build script.

I've amended the package and uploaded it to Launchpad.  Please look out
for the updated package 2.2.3-2biolinux2 and see if that sorts it.

Cheers,

TIM

On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:
> Anybody else experienced this error? Any ideas?
> Thanks 
> 
> Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br> escreveu:
>         Thanks a lot for the update.
>         
>         
>         However, it is trying to compile Jellyfish on the go. I'm
>         attaching the output. Relevant part:
>         
>         Trinity version: v2.0.6
>         ...
>         -------------------------------------------
>         ----------- Jellyfish  --------------------
>         -- (building a k-mer catalog from reads) --
>         -------------------------------------------
>         
>         Wednesday, October 14, 2015: 13:46:18
>         CMD: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223
>         --canonical  both.fa
>         mkdir: cannot create directory ?/usr/bin/.libs?: Permission
>         denied
>         /usr/bin/jellyfish: line 202:
>         cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such file or
>         directory
>         g++: error: sub_commands/jellyfish.o: No such file or
>         directory
>         g++: error: sub_commands/count_main.o: No such file or
>         directory
>         g++: error: sub_commands/info_main.o: No such file or
>         directory
>         g++: error: sub_commands/dump_main.o: No such file or
>         directory
>         g++: error: sub_commands/histo_main.o: No such file or
>         directory
>         g++: error: sub_commands/stats_main.o: No such file or
>         directory
>         g++: error: sub_commands/merge_main.o: No such file or
>         directory
>         g++: error: sub_commands/bc_main.o: No such file or directory
>         g++: error: sub_commands/query_main.o: No such file or
>         directory
>         g++: error: sub_commands/cite_main.o: No such file or
>         directory
>         g++: error: sub_commands/mem_main.o: No such file or directory
>         g++: error: jellyfish/merge_files.o: No such file or directory
>         g++: error: ./.libs/libjellyfish-2.0.so: No such file or
>         directorynError, cmd: /usr/bin/jellyfish count -t 15 -m 25 -s
>         14446126223  --canonical  both.fa died with ret 256
>         at /usr/lib/trinityrnaseq/Trinity line 2115.
>         
>         Trinity run failed. Must investigate error above.
>         
>         
>         On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran
>         <kirannbishwa01 at gmail.com> wrote:
>                 Thanks for the update !
>                 
>                 On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth
>                 <tbooth at ceh.ac.uk> wrote:
>                         Hi All,
>                         
>                         I've been doing a round of package updates on
>                         Bio-Linux 8 over the last
>                         week.  We now have both Mothur and Mira
>                         updated to the latest versions:
>                         
>                         mira-assembler package is version 4.9.5
>                         mothur package is version 1.36.1
>                         
>                         Both will be updated by the package updater.
>                         If you experience any
>                         problems or regressions with these new
>                         packages please let me know.
>                         
>                         I'm also pleased to say that the Trinity
>                         RNA-Seq De novo assembler has
>                         been added to the package repository
>                         (http://trinityrnaseq.github.io/).
>                         Various modifications have been made to
>                         Trinity to make it integrate
>                         nicely with the other packages on the system,
>                         so if you have problems
>                         running it please let me know and I'll check
>                         if it is maybe something
>                         that got messed up in the packaging.
>                         
>                         trinityrnaseq package is version 2.0.6
>                         
>                         To get it: sudo apt-get install trinityrnaseq
>                         then just type: "Trinity" (with the capital T)
>                         
>                         The credit for all this goes mainly to Michael
>                         and Andreas from the
>                         Debian Med project who maintain these packages
>                         in Debian.  I've been
>                         able to take what they made and backport it to
>                         Bio-Linux for you.
>                         
>                         Cheers,
>                         
>                         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
>                 
>                 
>                 
>                 
>                 -- 
>                 - Bish     
>                  
>                 
>                  
>                 
>                 _______________________________________________
>                 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  Tue Oct 27 14:23:01 2015
From: paumarc at gmail.com (=?UTF-8?Q?Pau_Marc_Mu=C3=B1oz_Torres?=)
Date: Tue, 27 Oct 2015 19:23:01 +0100
Subject: [Bio-Linux] Package GenomicRanges library
Message-ID: <CADFuJLgCzps3m1SeTtQ_6VwwQv+PDS9c-vvHs6BxatFC3zwjgw@mail.gmail.com>

Hello

  Has   Package GenomicRanges library from R been updated recently ? when i
execute a funtion of rapdir

library("RAPIDR")
makeBinnedCountsFile(c("nfamele1_sorted.bam","nfamele2_sorted.bam","nMALE1_sorted.bam","nMALE2_sorted.bam","T-SRR611848_1_sorted.bam"),c("nfamele1","nfamele2","nMALE1","nMALE2","T-SRR611848"),"binnedcounts.r",mask=NULL,k=20000)


I am getting the following error in a script that was working a month before

Error in unloadNamespace(package) :
  namespace ?GenomicRanges? is imported by ?RAPIDR?, ?GenomicAlignments?,
?Rsamtools? so cannot be unloaded
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc
= lib.loc,  :
  Package ?GenomicRanges? version 1.20.8 cannot be unloaded

what can i do?

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 tbooth at ceh.ac.uk  Wed Oct 28 08:29:17 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 28 Oct 2015 12:29:17 +0000
Subject: [Bio-Linux] Package GenomicRanges library
In-Reply-To: <CADFuJLgCzps3m1SeTtQ_6VwwQv+PDS9c-vvHs6BxatFC3zwjgw@mail.gmail.com>
References: <CADFuJLgCzps3m1SeTtQ_6VwwQv+PDS9c-vvHs6BxatFC3zwjgw@mail.gmail.com>
Message-ID: <1446035357.29689.89.camel@wllt1771.nerc-wallingford.ac.uk>

Hi,

I updated GenomicRanges along with all the core Bioconductor packages
when I made the RAPIDR package.  That was last month.  Since then there
is a new Bioconductor release but I'm not planning another round of
updates as it will take me days to sort out all the new packages.

Since I can't see your script I don't know why it is trying to unload
GenomicRanges but it makes sense that you can't do that while RAPIDR is
loaded.

If the script is a standalone script are you running it with the
--vanilla option to R?

Cheers,

TIM

On Tue, 2015-10-27 at 19:23 +0100, Pau Marc Mu?oz Torres wrote:
> Hello
> 
> 
>   Has   Package GenomicRanges library from R been updated
> recently ? when i execute a funtion of rapdir
> 
> 
> library("RAPIDR")
> makeBinnedCountsFile(c("nfamele1_sorted.bam","nfamele2_sorted.bam","nMALE1_sorted.bam","nMALE2_sorted.bam","T-SRR611848_1_sorted.bam"),c("nfamele1","nfamele2","nMALE1","nMALE2","T-SRR611848"),"binnedcounts.r",mask=NULL,k=20000)
> 
> 
> 
> 
> I am getting the following error in a script that was working a month
> before
> 
> 
> Error in unloadNamespace(package) : 
>   namespace ?GenomicRanges? is imported by ?RAPIDR?,
> ?GenomicAlignments?, ?Rsamtools? so cannot be unloaded
> Error in library(pkg, character.only = TRUE, logical.return = TRUE,
> lib.loc = lib.loc,  : 
>   Package ?GenomicRanges? version 1.20.8 cannot be unloaded
> 
> 
> what can i do?
> 
> 
> 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

-- 
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 morais at iq.usp.br  Wed Oct 28 14:34:59 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Wed, 28 Oct 2015 16:34:59 -0200
Subject: [Bio-Linux] Trinity added,
	Mothur and Mira updated - jellyfish problem
In-Reply-To: <1445967079.29689.31.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
 <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
 <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>
 <1445967079.29689.31.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7naRd6HfeeOVXerTwcwr4kyAXO9tCAifX8N753JzNg8wEQ@mail.gmail.com>

Thanks a lot, Tim!
This upgrade really fixes the Jellyfish part.
Now it breaks on Inchworm.
Apparently, trinity neither include Inchworm nor depends on another package
providing it. :-(

bash: /usr/lib/trinityrnaseq/Inchworm/bin//inchworm: No such file or
directory

Cheers,
    Carlos

On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Carlos,
>
> This looks to me like someone (maybe me) stuffed up the jellyfish
> package and installed the wrong file into /usr/bin.  It seems to be a
> simple typo in the build script.
>
> I've amended the package and uploaded it to Launchpad.  Please look out
> for the updated package 2.2.3-2biolinux2 and see if that sorts it.
>
> Cheers,
>
> TIM
>
> On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:
> > Anybody else experienced this error? Any ideas?
> > Thanks
> >
> > Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br> escreveu:
> >         Thanks a lot for the update.
> >
> >
> >         However, it is trying to compile Jellyfish on the go. I'm
> >         attaching the output. Relevant part:
> >
> >         Trinity version: v2.0.6
> >         ...
> >         -------------------------------------------
> >         ----------- Jellyfish  --------------------
> >         -- (building a k-mer catalog from reads) --
> >         -------------------------------------------
> >
> >         Wednesday, October 14, 2015: 13:46:18
> >         CMD: /usr/bin/jellyfish count -t 15 -m 25 -s 14446126223
> >         --canonical  both.fa
> >         mkdir: cannot create directory ?/usr/bin/.libs?: Permission
> >         denied
> >         /usr/bin/jellyfish: line 202:
> >         cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such file or
> >         directory
> >         g++: error: sub_commands/jellyfish.o: No such file or
> >         directory
> >         g++: error: sub_commands/count_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/info_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/dump_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/histo_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/stats_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/merge_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/bc_main.o: No such file or directory
> >         g++: error: sub_commands/query_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/cite_main.o: No such file or
> >         directory
> >         g++: error: sub_commands/mem_main.o: No such file or directory
> >         g++: error: jellyfish/merge_files.o: No such file or directory
> >         g++: error: ./.libs/libjellyfish-2.0.so: No such file or
> >         directorynError, cmd: /usr/bin/jellyfish count -t 15 -m 25 -s
> >         14446126223  --canonical  both.fa died with ret 256
> >         at /usr/lib/trinityrnaseq/Trinity line 2115.
> >
> >         Trinity run failed. Must investigate error above.
> >
> >
> >         On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran
> >         <kirannbishwa01 at gmail.com> wrote:
> >                 Thanks for the update !
> >
> >                 On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth
> >                 <tbooth at ceh.ac.uk> wrote:
> >                         Hi All,
> >
> >                         I've been doing a round of package updates on
> >                         Bio-Linux 8 over the last
> >                         week.  We now have both Mothur and Mira
> >                         updated to the latest versions:
> >
> >                         mira-assembler package is version 4.9.5
> >                         mothur package is version 1.36.1
> >
> >                         Both will be updated by the package updater.
> >                         If you experience any
> >                         problems or regressions with these new
> >                         packages please let me know.
> >
> >                         I'm also pleased to say that the Trinity
> >                         RNA-Seq De novo assembler has
> >                         been added to the package repository
> >                         (http://trinityrnaseq.github.io/).
> >                         Various modifications have been made to
> >                         Trinity to make it integrate
> >                         nicely with the other packages on the system,
> >                         so if you have problems
> >                         running it please let me know and I'll check
> >                         if it is maybe something
> >                         that got messed up in the packaging.
> >
> >                         trinityrnaseq package is version 2.0.6
> >
> >                         To get it: sudo apt-get install trinityrnaseq
> >                         then just type: "Trinity" (with the capital T)
> >
> >                         The credit for all this goes mainly to Michael
> >                         and Andreas from the
> >                         Debian Med project who maintain these packages
> >                         in Debian.  I've been
> >                         able to take what they made and backport it to
> >                         Bio-Linux for you.
> >
> >                         Cheers,
> >
> >                         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
> >
> >
> >
> >
> >                 --
> >                 - Bish
> >
> >
> >
> >
> >                 _______________________________________________
> >                 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
>
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From tbooth at ceh.ac.uk  Thu Oct 29 05:59:35 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 29 Oct 2015 09:59:35 +0000
Subject: [Bio-Linux] Trinity added,
 Mothur and Mira updated - Inchworm problem
In-Reply-To: <CAAzi7naRd6HfeeOVXerTwcwr4kyAXO9tCAifX8N753JzNg8wEQ@mail.gmail.com>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
 <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
 <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>
 <1445967079.29689.31.camel@wllt1771.nerc-wallingford.ac.uk>
 <CAAzi7naRd6HfeeOVXerTwcwr4kyAXO9tCAifX8N753JzNg8wEQ@mail.gmail.com>
Message-ID: <1446112775.29689.180.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Carlos,

Thanks for being the first proper tester on the Trinity package.  As
with Jellyfish the package was building correctly (hence passing
internal tests) but Inchworm never got packed into the final DEB file.
I've fixed the build rules and the new version is preparing on Launchpad
now.  Should appear as an update in about an hour.

Cheers,

TIM

On Wed, 2015-10-28 at 16:34 -0200, Carlos Morais wrote:
> Thanks a lot, Tim!
> 
> This upgrade really fixes the Jellyfish part.
> 
> Now it breaks on Inchworm.
> 
> Apparently, trinity neither include Inchworm nor depends on another
> package providing it. :-(
> 
> bash: /usr/lib/trinityrnaseq/Inchworm/bin//inchworm: No such file or
> directory
> 
> 
> Cheers,
> 
>     Carlos
> 
> 
> On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
>         Hi Carlos,
>         
>         This looks to me like someone (maybe me) stuffed up the
>         jellyfish
>         package and installed the wrong file into /usr/bin.  It seems
>         to be a
>         simple typo in the build script.
>         
>         I've amended the package and uploaded it to Launchpad.  Please
>         look out
>         for the updated package 2.2.3-2biolinux2 and see if that sorts
>         it.
>         
>         Cheers,
>         
>         TIM
>         
>         On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:
>         > Anybody else experienced this error? Any ideas?
>         > Thanks
>         >
>         > Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br>
>         escreveu:
>         >         Thanks a lot for the update.
>         >
>         >
>         >         However, it is trying to compile Jellyfish on the
>         go. I'm
>         >         attaching the output. Relevant part:
>         >
>         >         Trinity version: v2.0.6
>         >         ...
>         >         -------------------------------------------
>         >         ----------- Jellyfish  --------------------
>         >         -- (building a k-mer catalog from reads) --
>         >         -------------------------------------------
>         >
>         >         Wednesday, October 14, 2015: 13:46:18
>         >         CMD: /usr/bin/jellyfish count -t 15 -m 25 -s
>         14446126223
>         >         --canonical  both.fa
>         >         mkdir: cannot create directory ?/usr/bin/.libs?:
>         Permission
>         >         denied
>         >         /usr/bin/jellyfish: line 202:
>         >         cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such
>         file or
>         >         directory
>         >         g++: error: sub_commands/jellyfish.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/count_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/info_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/dump_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/histo_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/stats_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/merge_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/bc_main.o: No such file or
>         directory
>         >         g++: error: sub_commands/query_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/cite_main.o: No such file
>         or
>         >         directory
>         >         g++: error: sub_commands/mem_main.o: No such file or
>         directory
>         >         g++: error: jellyfish/merge_files.o: No such file or
>         directory
>         >         g++: error: ./.libs/libjellyfish-2.0.so: No such
>         file or
>         >         directorynError, cmd: /usr/bin/jellyfish count -t 15
>         -m 25 -s
>         >         14446126223  --canonical  both.fa died with ret 256
>         >         at /usr/lib/trinityrnaseq/Trinity line 2115.
>         >
>         >         Trinity run failed. Must investigate error above.
>         >
>         >
>         >         On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran
>         >         <kirannbishwa01 at gmail.com> wrote:
>         >                 Thanks for the update !
>         >
>         >                 On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth
>         >                 <tbooth at ceh.ac.uk> wrote:
>         >                         Hi All,
>         >
>         >                         I've been doing a round of package
>         updates on
>         >                         Bio-Linux 8 over the last
>         >                         week.  We now have both Mothur and
>         Mira
>         >                         updated to the latest versions:
>         >
>         >                         mira-assembler package is version
>         4.9.5
>         >                         mothur package is version 1.36.1
>         >
>         >                         Both will be updated by the package
>         updater.
>         >                         If you experience any
>         >                         problems or regressions with these
>         new
>         >                         packages please let me know.
>         >
>         >                         I'm also pleased to say that the
>         Trinity
>         >                         RNA-Seq De novo assembler has
>         >                         been added to the package repository
>         >                         (http://trinityrnaseq.github.io/).
>         >                         Various modifications have been made
>         to
>         >                         Trinity to make it integrate
>         >                         nicely with the other packages on
>         the system,
>         >                         so if you have problems
>         >                         running it please let me know and
>         I'll check
>         >                         if it is maybe something
>         >                         that got messed up in the packaging.
>         >
>         >                         trinityrnaseq package is version
>         2.0.6
>         >
>         >                         To get it: sudo apt-get install
>         trinityrnaseq
>         >                         then just type: "Trinity" (with the
>         capital T)
>         >
>         >                         The credit for all this goes mainly
>         to Michael
>         >                         and Andreas from the
>         >                         Debian Med project who maintain
>         these packages
>         >                         in Debian.  I've been
>         >                         able to take what they made and
>         backport it to
>         >                         Bio-Linux for you.
>         >
>         >                         Cheers,
>         >
>         >                         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
>         >
>         >
>         >
>         >
>         >                 --
>         >                 - Bish
>         >
>         >
>         >
>         >
>         >
>          _______________________________________________
>         >                 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 morais at iq.usp.br  Thu Oct 29 13:35:01 2015
From: morais at iq.usp.br (Carlos Morais)
Date: Thu, 29 Oct 2015 15:35:01 -0200
Subject: [Bio-Linux] Trinity added,
	Mothur and Mira updated - Inchworm problem
In-Reply-To: <1446112775.29689.180.camel@wllt1771.nerc-wallingford.ac.uk>
References: <1442227366.19889.114.camel@wllt1771.nerc-wallingford.ac.uk>
 <CANj1AG1SN43gZdBAow43zjMkP-1boLWimfAGr1NgqrXUoSsG_A@mail.gmail.com>
 <CAAzi7nb0uydHKNE339fDHGVEB1V1DHy=8ZDWrbcKX_HrdwYyFA@mail.gmail.com>
 <CAAzi7nbo=mG3HT=j3wez3nzRr1SUEra1993t+B5HEyhW9=3Gfg@mail.gmail.com>
 <1445967079.29689.31.camel@wllt1771.nerc-wallingford.ac.uk>
 <CAAzi7naRd6HfeeOVXerTwcwr4kyAXO9tCAifX8N753JzNg8wEQ@mail.gmail.com>
 <1446112775.29689.180.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <CAAzi7nY0OaVAdgrFACTJoJ9f4vs_ELSDV5ULWGe=MjXUrvs+Uw@mail.gmail.com>

Thanks again for the upgrade. I'm already running Trinity for 2 hours, and
it is now on Chrysalis phase. So, I'm assuming Inchworm part is now OK.
I'll let you know if it stumbles on another point.

On Thu, Oct 29, 2015 at 7:59 AM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Carlos,
>
> Thanks for being the first proper tester on the Trinity package.  As
> with Jellyfish the package was building correctly (hence passing
> internal tests) but Inchworm never got packed into the final DEB file.
> I've fixed the build rules and the new version is preparing on Launchpad
> now.  Should appear as an update in about an hour.
>
> Cheers,
>
> TIM
>
> On Wed, 2015-10-28 at 16:34 -0200, Carlos Morais wrote:
> > Thanks a lot, Tim!
> >
> > This upgrade really fixes the Jellyfish part.
> >
> > Now it breaks on Inchworm.
> >
> > Apparently, trinity neither include Inchworm nor depends on another
> > package providing it. :-(
> >
> > bash: /usr/lib/trinityrnaseq/Inchworm/bin//inchworm: No such file or
> > directory
> >
> >
> > Cheers,
> >
> >     Carlos
> >
> >
> > On Tue, Oct 27, 2015 at 3:31 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:
> >         Hi Carlos,
> >
> >         This looks to me like someone (maybe me) stuffed up the
> >         jellyfish
> >         package and installed the wrong file into /usr/bin.  It seems
> >         to be a
> >         simple typo in the build script.
> >
> >         I've amended the package and uploaded it to Launchpad.  Please
> >         look out
> >         for the updated package 2.2.3-2biolinux2 and see if that sorts
> >         it.
> >
> >         Cheers,
> >
> >         TIM
> >
> >         On Mon, 2015-10-26 at 08:41 -0200, Carlos Morais wrote:
> >         > Anybody else experienced this error? Any ideas?
> >         > Thanks
> >         >
> >         > Em 15/10/2015 12:28, "Carlos Morais" <morais at iq.usp.br>
> >         escreveu:
> >         >         Thanks a lot for the update.
> >         >
> >         >
> >         >         However, it is trying to compile Jellyfish on the
> >         go. I'm
> >         >         attaching the output. Relevant part:
> >         >
> >         >         Trinity version: v2.0.6
> >         >         ...
> >         >         -------------------------------------------
> >         >         ----------- Jellyfish  --------------------
> >         >         -- (building a k-mer catalog from reads) --
> >         >         -------------------------------------------
> >         >
> >         >         Wednesday, October 14, 2015: 13:46:18
> >         >         CMD: /usr/bin/jellyfish count -t 15 -m 25 -s
> >         14446126223
> >         >         --canonical  both.fa
> >         >         mkdir: cannot create directory ?/usr/bin/.libs?:
> >         Permission
> >         >         denied
> >         >         /usr/bin/jellyfish: line 202:
> >         >         cd: /build/jellyfish-sMXWdl/jellyfish-2.2.3: No such
> >         file or
> >         >         directory
> >         >         g++: error: sub_commands/jellyfish.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/count_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/info_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/dump_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/histo_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/stats_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/merge_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/bc_main.o: No such file or
> >         directory
> >         >         g++: error: sub_commands/query_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/cite_main.o: No such file
> >         or
> >         >         directory
> >         >         g++: error: sub_commands/mem_main.o: No such file or
> >         directory
> >         >         g++: error: jellyfish/merge_files.o: No such file or
> >         directory
> >         >         g++: error: ./.libs/libjellyfish-2.0.so: No such
> >         file or
> >         >         directorynError, cmd: /usr/bin/jellyfish count -t 15
> >         -m 25 -s
> >         >         14446126223  --canonical  both.fa died with ret 256
> >         >         at /usr/lib/trinityrnaseq/Trinity line 2115.
> >         >
> >         >         Trinity run failed. Must investigate error above.
> >         >
> >         >
> >         >         On Mon, Sep 14, 2015 at 10:00 AM, Bishwa Kiran
> >         >         <kirannbishwa01 at gmail.com> wrote:
> >         >                 Thanks for the update !
> >         >
> >         >                 On Mon, Sep 14, 2015 at 6:42 AM, Tim Booth
> >         >                 <tbooth at ceh.ac.uk> wrote:
> >         >                         Hi All,
> >         >
> >         >                         I've been doing a round of package
> >         updates on
> >         >                         Bio-Linux 8 over the last
> >         >                         week.  We now have both Mothur and
> >         Mira
> >         >                         updated to the latest versions:
> >         >
> >         >                         mira-assembler package is version
> >         4.9.5
> >         >                         mothur package is version 1.36.1
> >         >
> >         >                         Both will be updated by the package
> >         updater.
> >         >                         If you experience any
> >         >                         problems or regressions with these
> >         new
> >         >                         packages please let me know.
> >         >
> >         >                         I'm also pleased to say that the
> >         Trinity
> >         >                         RNA-Seq De novo assembler has
> >         >                         been added to the package repository
> >         >                         (http://trinityrnaseq.github.io/).
> >         >                         Various modifications have been made
> >         to
> >         >                         Trinity to make it integrate
> >         >                         nicely with the other packages on
> >         the system,
> >         >                         so if you have problems
> >         >                         running it please let me know and
> >         I'll check
> >         >                         if it is maybe something
> >         >                         that got messed up in the packaging.
> >         >
> >         >                         trinityrnaseq package is version
> >         2.0.6
> >         >
> >         >                         To get it: sudo apt-get install
> >         trinityrnaseq
> >         >                         then just type: "Trinity" (with the
> >         capital T)
> >         >
> >         >                         The credit for all this goes mainly
> >         to Michael
> >         >                         and Andreas from the
> >         >                         Debian Med project who maintain
> >         these packages
> >         >                         in Debian.  I've been
> >         >                         able to take what they made and
> >         backport it to
> >         >                         Bio-Linux for you.
> >         >
> >         >                         Cheers,
> >         >
> >         >                         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
> >         >
> >         >
> >         >
> >         >
> >         >                 --
> >         >                 - Bish
> >         >
> >         >
> >         >
> >         >
> >         >
> >          _______________________________________________
> >         >                 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
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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