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

[Debian Wiki]

Dear Wiki user,

You have subscribed to a wiki page or wiki category on "Debian Wiki" for change notification.

The "DebianMed/LiveCD" page has been changed by SteffenMoeller:
http://wiki.debian.org/DebianMed/LiveCD?action=diff&rev1=23&rev2=24

  
  For an easier copy and paste by avoiding line breaks
  {{{
- server="pc07.inb.uni-luebeck.de" # place your server here
+ server="some.server.com" # place your server here
  packages="libcv-dev|autodock|gromacs|ballview|autodocktools"
  packages="$packages|lvm2|openssh-server|openssh-client"
  packages="$packages|boinc-client|r-cran-qtl|r-recommended"
@@ -115, +115 @@

  
  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:
  
- THIS IS WORK IN PROGRESS
+  * manually verify that contrib and non-free are available
  
+ '''virtual:'''{{{
- {{{
- # manually verify that contrib and non-free are available
  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.
- # few packages we don't really need
- dpkg --purge mlocate
  
+  * Start with some packages in non-free, if this available
- # med-bio cannot be installed by apt-get without exceeding
- # 2G limit. The effort needs to be split. First a series
- # of packages that is only suggested by med-bio:
  
- if grep -q "non-free" /etc/apt/sources.list; then
+  '''virtual:'''{{{if grep -q "non-free" /etc/apt/sources.list; then
-   debfoster --upgrade clustalw phylip && apt-get clean
+    debfoster --upgrade clustalw phylip && apt-get clean
- fi
+  fi
+ }}}
  
- # a few package don't really need to be installed since
- # they are too graphical to be executed remotely
- notToInstall="ballview clustalx seaview pvm rasmol massxpert perlprimer xbitmaps ncbi-tools-x11 python-ballview treeviewx massxpert-data"
- for i in $notToInstall
- do
- dpkg --purge $i
- echo "$i purge" | dpkg --set-selections
- done
  
  # We now install packages within those recommended by Debian Med in smallish chunks
- 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"
+  '''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
+ for the moment. Their initial installation seems to be
+ inevitable, though.
+ 
+  '''virtual:'''{{{notToInstall="ballview clustalx seaview pvm rasmol massxpert perlprimer xbitmaps ncbi-tools-x11 python-ballview treeviewx massxpert-data"
+ for i in $notToInstall
+ do
+   dpkg --purge $i
+   echo "$i hold" | dpkg --set-selections
+ done
+ }}}
  
  # add remaining core packages && again save disk space
- yes | debfoster --upgrade med-bio && apt-get clean
  
- 
+  '''virtual:'''{{{
+ apt-get install med-bio && 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
  
+ apt-get --yes install --no-install-recommends octave
+ apt-get clean
+ 
+ apt-get --no-install-recommends med-bio-dev med-bio
+ }}}
+ 
+  * few packages we don't really need
+ 
+ '''virtual:''' {{{
+ for i in mlocate $(dpkg -l "*-doc" | grep ^ii | awk '{print $2}')
+ do
+    dpkg --purge $i && echo "$i hold"|dpkg --set-selections
+ done
+ }}}
+ 
+  * To "round it all up" and since some space is still available
+  '''virtual:'''{{{
+ apt-get --yes install mysql-client r-cran-rmysql libcv-dev
+ apt-get clean
+ apt-get autoremove
+ }}}
+