[Debian Wiki] Update of "BOINC/ServerGuide" by SteffenMoeller

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The "BOINC/ServerGuide" page has been changed by SteffenMoeller:
http://wiki.debian.org/BOINC/ServerGuide?action=diff&rev1=93&rev2=94

Comment:
update on preparatory steps

  === Step 1: Prepare the server ===
  
  All the above instructions were basically preparing for this:
-  * follow the instructions from above to create a working BOINC server web site
+  * follow the above description to create a working BOINC server web site
-  * follow the instructions from above to create the wrapper as an application
+  * follow the [[http://users.ox.ac.uk/~jesu1458/docker/|external online instructions]] to create the wrapper as an application
+ 
+   
   * do the following to get the autodock application as an executing tool
    * ?
    * ?
  
  === Step 2: Prepare the biology ===
  
- This step was not changed with respect to the original ''docker'' script. A few file locations have been modified. This just slightly adapted version of its "upper half" is kept [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;h=973851a2eb4d4890909d08386c070456e8c582c9;hb=HEAD|here]] ([[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;h=973851a2eb4d4890909d08386c070456e8c582c9;hb=HEAD|download]]).
+ This step was not changed with respect to the original ''docker'' script. A few file locations have been modified. This just slightly adapted version of its "upper half" is kept [[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;h=973851a2eb4d4890909d08386c070456e8c582c9;hb=HEAD|here]] ([[http://anonscm.debian.org/gitweb/?p=pkg-boinc/scripts.git;a=blob;f=server-examples/autodock/dock-pre.sh;hb=HEAD|download]]).
  
   * install Debian packages: autodocktools autodock autogrid
-  * follow the ''docker'' [[http://users.ox.ac.uk/~jesu1458/docker/|web tutorial]] for downloading the ligand files
+  * follow the ''docker'' [[http://users.ox.ac.uk/~jesu1458/docker/|web tutorial]] for
-  * follow the "upper half" of the ''docker'' script for preparing the receptor and the ligands for docking 
- 
- It is suggested to really go through the script line by line and not to just execute it.
+   * download receptor from http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=2RH1
+   * reduce to first 5 transmembrane helices
+   * prepare docking with AutoDockTools (start runAdt instead of adt)
+    * add hydrogens
+    * specify grid
+   * retrieving ligands
+  * follow the "upper half" of the ''docker'' script for preparing the receptor and the ligands for docking. It is suggested to really go through the script line by line and not to just execute it:
+   * split .mol2 ligand collection into many files
+   * name each correctly
  
  === Step 3: Submit jobs to BOINC server ===