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revision 1.11, Fri Jul 30 22:01:21 2004 UTC revision 1.12, Thu Aug 5 23:26:06 2004 UTC
# Line 90  Line 90 
90  /Volumes/Backup is a backup disk.  Then,  /Volumes/Backup is a backup disk.  Then,
91  <br>  <br>
92  <pre>  <pre>
93          cp -pRP /Users/fig/FIGdisk/FIG/Data /Volumes/Backup/Data.Backup          cp -pRP ~/FIGdisk/FIG/Data /Volumes/Backup/Data.Backup
94          gzip -r /Volumes/Backup/Data.Backup          gzip -r /Volumes/Backup/Data.Backup
95  </pre>  </pre>
96  <br>  <br>
# Line 705  Line 705 
705  We anticipate that at least one major center (Argonne National Lab) and, perhaps, more will create well-defined  We anticipate that at least one major center (Argonne National Lab) and, perhaps, more will create well-defined
706  interfaces for handling high-volume requests.  At FIG, we will maintain a set of instructions on how to set up  interfaces for handling high-volume requests.  At FIG, we will maintain a set of instructions on how to set up
707  your configuration to exploit these resources.  your configuration to exploit these resources.
708    <p>
709    No matter how you produce the new similarities, they need to be added
710    as a file in the <b>FIGdisk/FIG/Data/NewSims</b> directory.  Then, you
711    need to index these similarities using
712    <pre>
713            index_sims ~/FIGdisk/FIG/Data/NewSims/XXXX
714    </pre>
715    where XXXX is the file you added.  If you have more than one such
716    file, just put in several arguments for the command.  This will
717    "index" the similarities in that any of the new PEGs which have
718    similarities connecting them to other PEGs from the existing genomes
719    can now be displayed.  However, the connection from the existing
720    genomes to the new PEGs does not yet exist (we call these the "flips"
721    of the computed sims).  To get this ability, you need to go through a
722    process that will make your system unavailable for a period (and, it
723    will produce a substantial load on your system for a day or so, while
724    the SEED sorts, sifts, inserts, and generally plays with the "flips").
725    <br>
726    The extra steps you need to take to make a fully functional version
727    are as follows:
728    <ol>
729    <li>
730    First, you need to run
731    <pre>
732            update_sims ~/FIGdisk/FIG/Data/Global/peg.synonyms 300 ~/FIGdisk/FIG/Data/Sims ~/Tmp/FlippedSims ~/FIGdisk/FIG/Data/NewSims/*
733    </pre>
734    This should produce updated similarity files in a VERY BIG directory
735    that we happened to put at <i>~/Tmp/Flipped</i> (but, which you could
736    put anywhere).  This may run as much as a day or so (and you can watch
737    its progress as it updates the similarity files).
738    <li>The next step is to replace the existing similarity files with the
739    newly computed ones.  You need to make the SEED unavailable (via the
740    <b>SEED Control Panel</b>.
741    <li>Then, blow away the existing similarities using something like
742    <pre>
743            rm ~/FIGdisk/FIG/Data/Sims/*
744            rm ~/FIGdisk/FIG/Data/NewSims/*
745            cp ~/Tmp/FlippedSims/* ~/FIGdisk/FIG/Data/Sims
746            rm -r ~/Tmp/FlippedSims
747    </pre>
748    There are several ways to do this.  You might want to save the old
749    similarities somewhere.  You might be able to move (rather than copy),
750    the similarities.  Whatever suits you.
751    <li> Then run
752    <pre>
753            index_sims
754    </pre>
755    to re-index all of the similarities, and you should be fully
756    operational.
757    </ol>
758    <br>
759    
760  <h2 id="deleting_genomes">Deleting Genomes from a Version of the SEED</h2>  <h2 id="deleting_genomes">Deleting Genomes from a Version of the SEED</h2>
761    
# Line 734  Line 785 
785  the path to the current Data directory.  The third argument specifies the name of a directory  the path to the current Data directory.  The third argument specifies the name of a directory
786  that is created holding the extraction.  Thus,  that is created holding the extraction.  Thus,
787  <pre>  <pre>
788          extract_genomes unrestricted /Users/fig/FIGdisk/FIG/Data /Volumes/Tmp/ExtractedData          extract_genomes unrestricted ~/FIGdisk/FIG/Data /Volumes/Tmp/ExtractedData
789  </pre>  </pre>
790  would created the extracted Data directory for you.  If you wish to then produce a fully distributable  would created the extracted Data directory for you.  If you wish to then produce a fully distributable
791  version of the SEED from the existing version and the extracted Data directory, you would  version of the SEED from the existing version and the extracted Data directory, you would
792  use  use
793  <pre>  <pre>
794          make_a_SEED /Users/fig/FIGdisk /Volumes/Tmp/ExtractedData /Volumes/MyFriend/FIGdisk.ReadyToGo          make_a_SEED ~/FIGdisk /Volumes/Tmp/ExtractedData /Volumes/MyFriend/FIGdisk.ReadyToGo
795          rm -rf /Volumes/Tmp/ExtractedData          rm -rf /Volumes/Tmp/ExtractedData
796  </pre>  </pre>
797    

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