Running DOCK

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Running DOCK

  • modify INDOCK and set up the desired directory structure – either manually or by running mksdir3.csh N1 N2 Type, where N1 is the identifier of the library (1: lead-like; 2: fragment-like), N2 is the number of chunks (i.e., jobs you can run in parallel), and Type is the category of library (i.e., bysubset, byvendor, etc).
  • if it hasn't been generated by a script, create the file dirlist, which conatins the list of the directories (i.e., chunks of the database) that you want to dock.
  • if you plan to use any of John's scripts in the downstream processing, leave the output file prefixes at test..
  • take care that the paths to the .db.gz files in split_database_index do not get too long. If they do, go via links.
  • submit the calculations to the cluster with startdockbks3 DIR, where DIR indicates the directory in which your data (most importantly, dirlist; usually it will be '.') resides.