[med-svn] [Debian Wiki] Update of "DebianMed/LiveCD" by SteffenMoeller

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The "DebianMed/LiveCD" page has been changed by SteffenMoeller:
http://wiki.debian.org/DebianMed/LiveCD?action=diff&rev1=24&rev2=25

  
  Conceptionally, there is no difference in preparing for local or remote virtual images. To learn more about it, 
   * see the walk-through on [[euca2ools]]
-  * the description for VMbuilder for Debian was never completed. But with Dominique's [[Cloud/CreateImage|instructions]] on how to create a cloud image, one does not miss that much any more.
+  * the [[Cloud/CreateImage|instructions]] on how to create a cloud image
+  * maybe reread through the concept of blends and how the community decides uttermost pragmatically on what might go together in one cloud image
  
  From the user's perspective, the image on the cloud shall be different. One does not expect much interaction with that for instance, alone since one is likely to pay for traffic. Hence, all interactive tools should go, or mostly go. This will also help saving disc space and thus increase responsiveness upon the start of an instance. All the following code shall be executed within an empty cloud image - or just any image that shall be filled:
  
   * manually verify that contrib and non-free are available
- 
- '''virtual:'''{{{
+  '''virtual:'''{{{
  apt-get update
  }}}
  
  The whole of med-bio would just fit on a 2GB image, but not both the /var/cache/apt/archives of   downloaded .debs 'and' the final installatin. With the current version of apt-get, one needs to install in chunks and delete files earlier. Yes, this is some criticism on apt-get, but I cannot fix this myself.
  
   * Start with some packages in non-free, if this available
- 
   '''virtual:'''{{{if grep -q "non-free" /etc/apt/sources.list; then
     debfoster --upgrade clustalw phylip && apt-get clean
   fi
  }}}
  
+ The invocation of "apt-get" is associated with some little constant overhead. We cannot install all at once, but don't want to install them one by one either. Sigh.
  
- # We now install packages within those recommended by Debian Med in smallish chunks
+  * Install packages within those recommended by Debian Med in smallish chunks
   '''virtual:'''{{{for i in "r-recommended r-cran-qtl" "mustang muscle t-coffee kalign boxshade" "infernal hmmer" emboss "autodock autogrid" "wise exonerate" "blast2 ncbi-tools-bin" "libbiojava-java bioperl bioperl-run" "python-biopython openbabel" "libball1.3 python-ball"
  do 
    apt-get --yes install $i && apt-get clean
  done
  }}}
  
+ A few package don't really need to be installed since they are too graphical to be executed remotely. Their initial installation seems to be inevitable, though.
- A few package don't really need to be installed since
- they are too graphical to be executed remotely
- for the moment. Their initial installation seems to be
- inevitable, though.
  
+  * remove GUI-centric programs and avoid reinstallation as a recommended dependency
   '''virtual:'''{{{notToInstall="ballview clustalx seaview pvm rasmol massxpert perlprimer xbitmaps ncbi-tools-x11 python-ballview treeviewx massxpert-data"
  for i in $notToInstall
  do
@@ -151, +149 @@

  done
  }}}
  
- # add remaining core packages && again save disk space
+  * add remaining core packages && again save disk space
- 
   '''virtual:'''{{{
- apt-get install med-bio && apt-get clean
+ apt-get install med-bio med-statistics && apt-get clean
  }}}
  
   * Octave is too big to be installed with all its dependencies in one go. The effort is split by again installing a series of packages separately that are of interest on their own
- 
   '''virtual:'''{{{
  apt-get --yes install libqhull5 texinfo
  apt-get clean
@@ -170, +166 @@

  }}}
  
   * few packages we don't really need
- 
- '''virtual:''' {{{
+  '''virtual:''' {{{
  for i in mlocate $(dpkg -l "*-doc" | grep ^ii | awk '{print $2}')
  do
     dpkg --purge $i && echo "$i hold"|dpkg --set-selections