From azlobin at lumc.edu  Wed Mar  5 16:54:42 2014
From: azlobin at lumc.edu (Andrei Zlobin)
Date: Wed, 5 Mar 2014 15:54:42 -0600
Subject: [Bio-Linux] NGS and GALAXY
Message-ID: <531748C2020000200002EEC4@gwgwia1.luhs.org>

Dear Experts,
I installed last version of Bio (on February) as a dual setup on a computer.
I need to work with data of RNA-Seq. Experiments were done on HiSeq2500 unit. I have all data, they are all right. I downloaded Bio-Linux fron DVD
disk,  installed on a computer, with 8G RAM, 4 core processor and 128 G disk space. I did update as recommended, all went fine.
 
1. I am using NGS programs, but problems start from very beginning, I can not  upload files, (they are big~3GB), when I press "execute" panel with
arrow blinks, (on right pane) but nothing is happening and it may continue for 48 h! If I use (usegalaxy.org with the same file all is all right.) I can
upload small files ~.5G but,
2. If file is small I can not run it because when I need to chose reference geneome, in option   "GENOME", it doesn't work-nothing is in the frame, (when I upload file option GENOME works fine). Also in some NGS programs option to choose file doesn't work. It doesn't see file at all.  
As far as I can see (I am a molecular biologist, not a IT tech) this is the problem of installation. I tried to read manuals, but it sad open file XYZ.loc (or ABC.ini)  ore something like this, which I can not fined at all, nothing like this.
Any suggestions?
Thanks
Andrew
 
 
 
Can you explain what's wrong?
 
 
-----------------------------
Andrew Zlobin, Ph.D
Cancer Center, Loyola University Medical Center
2160 S. First Ave, Bldg 112,
Rm 323,
Maywood, IL 60153
(708) 327-3122 
(708) 327-3342 fax
mailto:azlobin at lumc.edu 
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From tbooth at ceh.ac.uk  Mon Mar 10 10:23:51 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 10 Mar 2014 14:23:51 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
Message-ID: <1394461431.3551.66.camel@balisaur>

Dear Bio-Linux users,

I've packaged the latest QIIME 1.8.0 which came out late last year.  The
package will appear in available updates later today.  Please be aware
that this has some differences from the previous release, particularly
that it uses Emperor by default rather than KiNG for 3D plots (though
the latter can still be used).  You may need to modify your procedures
or scripts.  The QIIME tutorial in the introductory course notes is
still being updated to reflect the changes.

I have also now included the Greengenes core set and lanemask files within
the qiime-data package as these have not changed in months and they are
now included as standard with other QIIME releases.

I still can't include USearch or Rtax due to copyright restrictions, and
I've not bothered packaging pplacer or sourcetracker yet but if anyone
is really keen to get these included please let me know.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705



From Jason.Bramwell at ahvla.gsi.gov.uk  Tue Mar 11 07:05:55 2014
From: Jason.Bramwell at ahvla.gsi.gov.uk (Bramwell, Jason)
Date: Tue, 11 Mar 2014 11:05:55 -0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <1394461431.3551.66.camel@balisaur>
References: <1394461431.3551.66.camel@balisaur>
Message-ID: <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>

Tim,
What do I have to do to get these (and other) updates? The documentation
is saying that updates should occur every night but this does not seem
to be the case for me (689 packaged required yesterday and 689 packages
still required today). So far I've been running apt-get update/upgrade
but is this the correct way or is there a 'bio-linux' way of doing this?

So far when I update a fresh install there are 689 update packages which
I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
held back. Am I doing this correctly or should i be following an
alternate method?

Thanks
Jason Bramwell

-----Original Message-----
From: Tim Booth [mailto:tbooth at ceh.ac.uk] 
Sent: 10 March 2014 14:24
To: Bio-Linux mailing list
Subject: [Bio-Linux] Updated QIIME package 1.8.0

Dear Bio-Linux users,

I've packaged the latest QIIME 1.8.0 which came out late last year.  The
package will appear in available updates later today.  Please be aware
that this has some differences from the previous release, particularly
that it uses Emperor by default rather than KiNG for 3D plots (though
the latter can still be used).  You may need to modify your procedures
or scripts.  The QIIME tutorial in the introductory course notes is
still being updated to reflect the changes.

I have also now included the Greengenes core set and lanemask files
within the qiime-data package as these have not changed in months and
they are now included as standard with other QIIME releases.

I still can't include USearch or Rtax due to copyright restrictions, and
I've not bothered packaging pplacer or sourcetracker yet but if anyone
is really keen to get these included please let me know.

Cheers,

TIM

--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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This email and any attachments is intended for the named recipient only.
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Whilst this email and associated attachments will have been checked for known viruses whilst within AHVLA systems we can accept no responsibility once it has left our systems.
Communications on AHVLA computer systems may be monitored and/or recorded to secure the effective operation of the system and for other lawful purposes.



From tony.travis at abdn.ac.uk  Tue Mar 11 07:29:19 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 11 Mar 2014 11:29:19 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
References: <1394461431.3551.66.camel@balisaur>
 <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
Message-ID: <531EF38F.1000507@abdn.ac.uk>

On 11/03/14 11:05, Bramwell, Jason wrote:
> Tim,
> What do I have to do to get these (and other) updates? The documentation
> is saying that updates should occur every night but this does not seem
> to be the case for me (689 packaged required yesterday and 689 packages
> still required today). So far I've been running apt-get update/upgrade
> but is this the correct way or is there a 'bio-linux' way of doing this?

Hi, Jason.

You can do 'unattended' upgrades if you want, using the "upgrade-system"
package. This updates the APT database, then downloads and installs
upgrades. However, you *MUST* edit its configuration file or
"upgrade-system" will remove 'redundant' packages too aggressively.
Change the "deborphan" priority to 6:

  sudo -i
  apt-get install upgrade-system
  vim /etc/upgrade-system.conf
  ...
  ORPHANOPTS="--guess-all --libdevel --priority=6"
  ...

The "upgrade-system" command is run daily from:

  /etc/cron.daily/upgrade-system

This only updates the databases, but you can edit it to run
"upgrade-system" once a day by adding the command at the end of the cron
job:

  vim /etc/cron.daily/upgrade-system
  ...
  upgrade-system
  #EOF
  ...

> So far when I update a fresh install there are 689 update packages which
> I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> held back. Am I doing this correctly or should i be following an
> alternate method?

Before you upgrade anything, I recommend installing "aptitude" and using
it to check the consistency of your APT database:

  apt-get install aptitude
  aptitude update
  aptitude -f install

Ubuntu no longer installs "aptitude" by default, but it is recommended
by Debian for managing packages from the command-line:

  https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html

> 8.1.3 aptitude
>
> aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
>
> aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
>
>     aptitude offers easy access to all versions of a package.
>
>     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
>
>     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
>
>     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
>
>     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
>
> You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
>
> Note that aptitude is the preferred program for daily package management from console.

You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
Interface). If you want to you can, but I don't recommend it. The main
reason I prefer aptitude is that it is good at fixing broken packages.

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
The University of Aberdeen is a charity registered in Scotland, No SC013683.


From tbooth at ceh.ac.uk  Tue Mar 11 07:53:23 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 11 Mar 2014 11:53:23 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <531EF38F.1000507@abdn.ac.uk>
References: <1394461431.3551.66.camel@balisaur>
 <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
 <531EF38F.1000507@abdn.ac.uk>
Message-ID: <1394538803.3551.107.camel@balisaur>

Hi Tony and Jason,

Upgrade-system may be worth trying but Bio-Linux has always used
"cron-apt" for automated updates so Jason will also need to disable that
before switching to "upgrade-system".  I've switched off unattended
upgrades on my own machine and I just use the graphical update manager
that pops up in Unity so that approach should also be fine, as should
running apt-get or aptitude or synaptic or any of the other package
managers.

I personally don't like the "aptitude" software and in my opinion they
removed it from Ubuntu for good reason - it breaks as many things as it
fixes.  I jsut use apt-get.

My advice would be to run "apt-get dist-upgrade" and if that gives an
error when working out which packages to upgrade please post the
details.  Normally you'll find that there are one or two packages
gumming up the works and once these are manually updated the rest all
follows.  Aptitude is supposed to work these things out more
intelligently than apt-get but I'm always wary of intelligent software.

Cheers,

TIM

On Tue, 2014-03-11 at 11:29 +0000, Tony Travis wrote:
> On 11/03/14 11:05, Bramwell, Jason wrote:
> > Tim,
> > What do I have to do to get these (and other) updates? The documentation
> > is saying that updates should occur every night but this does not seem
> > to be the case for me (689 packaged required yesterday and 689 packages
> > still required today). So far I've been running apt-get update/upgrade
> > but is this the correct way or is there a 'bio-linux' way of doing this?
> 
> Hi, Jason.
> 
> You can do 'unattended' upgrades if you want, using the "upgrade-system"
> package. This updates the APT database, then downloads and installs
> upgrades. However, you *MUST* edit its configuration file or
> "upgrade-system" will remove 'redundant' packages too aggressively.
> Change the "deborphan" priority to 6:
> 
>   sudo -i
>   apt-get install upgrade-system
>   vim /etc/upgrade-system.conf
>   ...
>   ORPHANOPTS="--guess-all --libdevel --priority=6"
>   ...
> 
> The "upgrade-system" command is run daily from:
> 
>   /etc/cron.daily/upgrade-system
> 
> This only updates the databases, but you can edit it to run
> "upgrade-system" once a day by adding the command at the end of the cron
> job:
> 
>   vim /etc/cron.daily/upgrade-system
>   ...
>   upgrade-system
>   #EOF
>   ...
> 
> > So far when I update a fresh install there are 689 update packages which
> > I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> > held back. Am I doing this correctly or should i be following an
> > alternate method?
> 
> Before you upgrade anything, I recommend installing "aptitude" and using
> it to check the consistency of your APT database:
> 
>   apt-get install aptitude
>   aptitude update
>   aptitude -f install
> 
> Ubuntu no longer installs "aptitude" by default, but it is recommended
> by Debian for managing packages from the command-line:
> 
>   https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html
> 
> > 8.1.3 aptitude
> >
> > aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
> >
> > aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
> >
> >     aptitude offers easy access to all versions of a package.
> >
> >     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
> >
> >     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
> >
> >     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
> >
> >     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
> >
> > You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
> >
> > Note that aptitude is the preferred program for daily package management from console.
> 
> You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
> Interface). If you want to you can, but I don't recommend it. The main
> reason I prefer aptitude is that it is good at fixing broken packages.
> 
> HTH,
> 
>   Tony.
> 
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> The University of Aberdeen is a charity registered in Scotland, No SC013683.
> _______________________________________________
> 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>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From jttkim at googlemail.com  Tue Mar 11 09:09:45 2014
From: jttkim at googlemail.com (Jan Kim)
Date: Tue, 11 Mar 2014 13:09:45 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <1394538803.3551.107.camel@balisaur>
References: <1394461431.3551.66.camel@balisaur>
 <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
 <531EF38F.1000507@abdn.ac.uk> <1394538803.3551.107.camel@balisaur>
Message-ID: <20140311130944.GA2465@localhost>

Dear Tim,

On Tue, Mar 11, 2014 at 11:53:23AM +0000, Tim Booth wrote:
> Hi Tony and Jason,
> 
> Upgrade-system may be worth trying but Bio-Linux has always used
> "cron-apt" for automated updates so Jason will also need to disable that
> before switching to "upgrade-system".  I've switched off unattended
> upgrades on my own machine and I just use the graphical update manager
> that pops up in Unity so that approach should also be fine, as should
> running apt-get or aptitude or synaptic or any of the other package
> managers.
> 
> I personally don't like the "aptitude" software and in my opinion they
> removed it from Ubuntu for good reason - it breaks as many things as it
> fixes.  I jsut use apt-get.

out of interest, what's wrong with aptitude? I use that pretty much in
the way you use the graphical package manager, and my understanding is
that it's based on the same Debian package management libraries as
apt-get, dpkg and the GUI based stuff.

Best regards, Jan

> My advice would be to run "apt-get dist-upgrade" and if that gives an
> error when working out which packages to upgrade please post the
> details.  Normally you'll find that there are one or two packages
> gumming up the works and once these are manually updated the rest all
> follows.  Aptitude is supposed to work these things out more
> intelligently than apt-get but I'm always wary of intelligent software.
> 
> Cheers,
> 
> TIM
> 
> On Tue, 2014-03-11 at 11:29 +0000, Tony Travis wrote:
> > On 11/03/14 11:05, Bramwell, Jason wrote:
> > > Tim,
> > > What do I have to do to get these (and other) updates? The documentation
> > > is saying that updates should occur every night but this does not seem
> > > to be the case for me (689 packaged required yesterday and 689 packages
> > > still required today). So far I've been running apt-get update/upgrade
> > > but is this the correct way or is there a 'bio-linux' way of doing this?
> > 
> > Hi, Jason.
> > 
> > You can do 'unattended' upgrades if you want, using the "upgrade-system"
> > package. This updates the APT database, then downloads and installs
> > upgrades. However, you *MUST* edit its configuration file or
> > "upgrade-system" will remove 'redundant' packages too aggressively.
> > Change the "deborphan" priority to 6:
> > 
> >   sudo -i
> >   apt-get install upgrade-system
> >   vim /etc/upgrade-system.conf
> >   ...
> >   ORPHANOPTS="--guess-all --libdevel --priority=6"
> >   ...
> > 
> > The "upgrade-system" command is run daily from:
> > 
> >   /etc/cron.daily/upgrade-system
> > 
> > This only updates the databases, but you can edit it to run
> > "upgrade-system" once a day by adding the command at the end of the cron
> > job:
> > 
> >   vim /etc/cron.daily/upgrade-system
> >   ...
> >   upgrade-system
> >   #EOF
> >   ...
> > 
> > > So far when I update a fresh install there are 689 update packages which
> > > I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> > > held back. Am I doing this correctly or should i be following an
> > > alternate method?
> > 
> > Before you upgrade anything, I recommend installing "aptitude" and using
> > it to check the consistency of your APT database:
> > 
> >   apt-get install aptitude
> >   aptitude update
> >   aptitude -f install
> > 
> > Ubuntu no longer installs "aptitude" by default, but it is recommended
> > by Debian for managing packages from the command-line:
> > 
> >   https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html
> > 
> > > 8.1.3 aptitude
> > >
> > > aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
> > >
> > > aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
> > >
> > >     aptitude offers easy access to all versions of a package.
> > >
> > >     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
> > >
> > >     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
> > >
> > >     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
> > >
> > >     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
> > >
> > > You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
> > >
> > > Note that aptitude is the preferred program for daily package management from console.
> > 
> > You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
> > Interface). If you want to you can, but I don't recommend it. The main
> > reason I prefer aptitude is that it is good at fixing broken packages.
> > 
> > HTH,
> > 
> >   Tony.
> > 
> > --
> > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> > The University of Aberdeen is a charity registered in Scotland, No SC013683.
> > _______________________________________________
> > 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>
> NERC Environmental Bioinformatics Centre 
> 
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB 
> 
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*


From tony.travis at abdn.ac.uk  Tue Mar 11 08:10:50 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 11 Mar 2014 12:10:50 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <1394538803.3551.107.camel@balisaur>
References: <1394461431.3551.66.camel@balisaur>
 <BAD9EF24BE0C8140847F231A462B49D00561FACB@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
 <531EF38F.1000507@abdn.ac.uk> <1394538803.3551.107.camel@balisaur>
Message-ID: <531EFD4A.7070204@abdn.ac.uk>

On 11/03/14 11:53, Tim Booth wrote:
> [...] Aptitude is supposed to work these things out more
> intelligently than apt-get but I'm always wary of intelligent
> software.

Hi, Tim.

Over the years, I've found that "aptitude" has got me out of more holes
than it has got me into ;-)

In particular, I use "aptitude -f" to check APT database consistency.

I agree it doesn't make a lot of difference how you install packages
manually, but my experience is that "apt-get" or "dpkg" both allow some
odd package installations that leave the APT database inconsistent...

I'm not quite sure why they removed it from Ubuntu: It was probably
removed along with "synaptic" to encourage people to use the Canonical
'App' store to install packages instead!

Bye,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
The University of Aberdeen is a charity registered in Scotland, No SC013683.


From tony.travis at abdn.ac.uk  Tue Mar 11 08:16:07 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 11 Mar 2014 12:16:07 +0000
Subject: [Bio-Linux] Updated QIIME package 1.8.0
In-Reply-To: <20140311130944.GA2465@localhost>
References: <1394461431.3551.66.camel@balisaur>
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On 11/03/14 13:09, Jan Kim wrote:
> [...]
> out of interest, what's wrong with aptitude? I use that pretty much in
> the way you use the graphical package manager, and my understanding is
> that it's based on the same Debian package management libraries as
> apt-get, dpkg and the GUI based stuff.

Hi, Jan.

Yes, it is, but "aptitude" is better at fixing broken dependencies.

However, I *really* don't like the "aptitude" TUI - I use "synaptic" for
that sort of task. I mainly use "aptitude -f" to make sure the APT
database is consistent before installing packages and also when I'm
troubleshooting a broken system. I switched to "aptitude" because it's
recommended by Debian for managing packages from the command-line.

Bye,

  Tony.
--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
The University of Aberdeen is a charity registered in Scotland, No SC013683.


From tbooth at ceh.ac.uk  Tue Mar 11 09:10:28 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 11 Mar 2014 13:10:28 +0000
Subject: [Bio-Linux] aptitude vs apt-get vs Synaptic vs ...
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Message-ID: <1394543428.3551.164.camel@balisaur>

Hi,

I think this is a bit like the TCSH vs BASH vs ZSH debate, and it's
really a matter of preference.

The important thing to remember is that all these applications use the
same DPKG under the hood, and while they may select slightly different
package combinations to install or remove in some circumstances they
will all install the packages correctly and you can use whichever works
best for you or indeed switch between them.  And once you have verified
your installation is consistent (with "aptitude -f or "apt-get -f check"
or however) you can be confident that all pending installations
completed successfully and all required dependencies are present.

Cheers,

TIM

On Tue, 2014-03-11 at 13:09 +0000, Jan Kim wrote:
> Dear Tim,
> 
> On Tue, Mar 11, 2014 at 11:53:23AM +0000, Tim Booth wrote:
> > Hi Tony and Jason,
> > 
> > Upgrade-system may be worth trying but Bio-Linux has always used
> > "cron-apt" for automated updates so Jason will also need to disable that
> > before switching to "upgrade-system".  I've switched off unattended
> > upgrades on my own machine and I just use the graphical update manager
> > that pops up in Unity so that approach should also be fine, as should
> > running apt-get or aptitude or synaptic or any of the other package
> > managers.
> > 
> > I personally don't like the "aptitude" software and in my opinion they
> > removed it from Ubuntu for good reason - it breaks as many things as it
> > fixes.  I jsut use apt-get.
> 
> out of interest, what's wrong with aptitude? I use that pretty much in
> the way you use the graphical package manager, and my understanding is
> that it's based on the same Debian package management libraries as
> apt-get, dpkg and the GUI based stuff.
> 
> Best regards, Jan
> 
> > My advice would be to run "apt-get dist-upgrade" and if that gives an
> > error when working out which packages to upgrade please post the
> > details.  Normally you'll find that there are one or two packages
> > gumming up the works and once these are manually updated the rest all
> > follows.  Aptitude is supposed to work these things out more
> > intelligently than apt-get but I'm always wary of intelligent software.
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Tue, 2014-03-11 at 11:29 +0000, Tony Travis wrote:
> > > On 11/03/14 11:05, Bramwell, Jason wrote:
> > > > Tim,
> > > > What do I have to do to get these (and other) updates? The documentation
> > > > is saying that updates should occur every night but this does not seem
> > > > to be the case for me (689 packaged required yesterday and 689 packages
> > > > still required today). So far I've been running apt-get update/upgrade
> > > > but is this the correct way or is there a 'bio-linux' way of doing this?
> > > 
> > > Hi, Jason.
> > > 
> > > You can do 'unattended' upgrades if you want, using the "upgrade-system"
> > > package. This updates the APT database, then downloads and installs
> > > upgrades. However, you *MUST* edit its configuration file or
> > > "upgrade-system" will remove 'redundant' packages too aggressively.
> > > Change the "deborphan" priority to 6:
> > > 
> > >   sudo -i
> > >   apt-get install upgrade-system
> > >   vim /etc/upgrade-system.conf
> > >   ...
> > >   ORPHANOPTS="--guess-all --libdevel --priority=6"
> > >   ...
> > > 
> > > The "upgrade-system" command is run daily from:
> > > 
> > >   /etc/cron.daily/upgrade-system
> > > 
> > > This only updates the databases, but you can edit it to run
> > > "upgrade-system" once a day by adding the command at the end of the cron
> > > job:
> > > 
> > >   vim /etc/cron.daily/upgrade-system
> > >   ...
> > >   upgrade-system
> > >   #EOF
> > >   ...
> > > 
> > > > So far when I update a fresh install there are 689 update packages which
> > > > I can install but then FastTree, Glimmer, Galaxy, Mira and QIIME are
> > > > held back. Am I doing this correctly or should i be following an
> > > > alternate method?
> > > 
> > > Before you upgrade anything, I recommend installing "aptitude" and using
> > > it to check the consistency of your APT database:
> > > 
> > >   apt-get install aptitude
> > >   aptitude update
> > >   aptitude -f install
> > > 
> > > Ubuntu no longer installs "aptitude" by default, but it is recommended
> > > by Debian for managing packages from the command-line:
> > > 
> > >   https://www.debian.org/doc/manuals/debian-faq/ch-pkgtools.en.html
> > > 
> > > > 8.1.3 aptitude
> > > >
> > > > aptitude is a package manager for Debian GNU/Linux systems that provides a frontend to the apt package management infrastructure. aptitude is a text-based interface using the curses library, it can be used to perform management tasks in a fast and easy way.
> > > >
> > > > aptitude provides the functionality of dselect and apt-get, as well as many additional features not found in either program:
> > > >
> > > >     aptitude offers easy access to all versions of a package.
> > > >
> > > >     aptitude makes it easy to keep track of obsolete software by listing it under "Obsolete and Locally Created Packages".
> > > >
> > > >     aptitude includes a fairly powerful system for searching particular packages and limiting the package display. Users familiar with mutt will pick up quickly, as mutt was the inspiration for the expression syntax.
> > > >
> > > >     aptitude can be used to install the predefined tasks available. For more information see tasksel, Section 8.1.5.
> > > >
> > > >     aptitude in full screen mode has su functionality embedded and can be run by a normal user. It will call su (and ask for the root password, if any) when you really need administrative privileges
> > > >
> > > > You can use aptitude through a visual interface (simply run aptitude) or directly from the command line. The command line syntax used is very similar to the one used in apt-get. For example, to install the foo package, you can run aptitude install foo.
> > > >
> > > > Note that aptitude is the preferred program for daily package management from console.
> > > 
> > > You do NOT have to run "aptitude" from a TUI (Full-Screen Text User
> > > Interface). If you want to you can, but I don't recommend it. The main
> > > reason I prefer aptitude is that it is good at fixing broken packages.
> > > 
> > > HTH,
> > > 
> > >   Tony.
> > > 
> > > --
> > > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> > > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> > > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> > > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
> > > The University of Aberdeen is a charity registered in Scotland, No SC013683.
> > > _______________________________________________
> > > 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>
> > NERC Environmental Bioinformatics Centre 
> > 
> > Centre for Ecology and Hydrology
> > Maclean Bldg, Benson Lane
> > Crowmarsh Gifford
> > Wallingford, England
> > OX10 8BB 
> > 
> > http://nebc.nerc.ac.uk
> > +44 1491 69 2705
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705