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1  <h1>Backing Up Your Data</h1>  <h1>SEED Administration</h1>
2    <p>This tutorial discusses a number of issues that you will need to know about
3      in order to install, share, and maintain your SEED installation.</p>
4    <h2>Backing Up Your Data</h2>
5  The data and code stored within the SEED are organized as follows:  The data and code stored within the SEED are organized as follows:
6  <pre>  <pre>
7          ~fig                                 on a Mac: /Users/fig; on Linux: /home/fig          ~fig                                 on a Mac: /Users/fig; on Linux: /home/fig
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11                                  Tmp          temporary files                                  Tmp          temporary files
12                                  Data         data in readable form                                  Data         data in readable form
13  </pre>  </pre>
14  <br>  <ol><li>
 <br>  
 <ol>  
 <li>  
15  The directory <b>FIGdisk</b> holds both the code and data for the  The directory <b>FIGdisk</b> holds both the code and data for the
16  SEED.  The data is loaded into a database system that stores the data  SEED.  The data is loaded into a database system that stores the data
17  in a location external to FIGdisk, but otherwise a running SEED is  in a location external to FIGdisk, but otherwise a running SEED is
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56  would be a reasonable way to make a backup.  The copy preserves  would be a reasonable way to make a backup.  The copy preserves
57  permissions, copies recursively, and does not follow symbolic links.  permissions, copies recursively, and does not follow symbolic links.
58  <br>  <br>
59  <h1>Copying a Version of the SEED</h1>  <h2>Copying a Version of the SEED</h2>
60    
61  To make a second copy of the SEED (either for a friend or for yourself), you should use tar  To make a second copy of the SEED (either for a friend or for yourself), you should use tar
62  to preserve a few symbolic links (which are relative, not absolute; this means that they can  to preserve a few symbolic links (which are relative, not absolute; this means that they can
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88      <td>&nbsp;</td>      <td>&nbsp;</td>
89    </tr>    </tr>
90    <tr>    <tr>
91        <td><font face="Courier New, Courier, mono">bash</font></td>
92        <td>Switch to using the bash shell</td>
93      </tr>
94      <tr>
95      <td><font face="Courier New, Courier, mono">cd FIGdisk</font></td>      <td><font face="Courier New, Courier, mono">cd FIGdisk</font></td>
96      <td>&nbsp;</td>      <td>&nbsp;</td>
97    </tr>    </tr>
98    <tr>    <tr>
99      <td><font face="Courier New, Courier, mono">cp CURRENT_RELEASE DEFAULT_RELEASE</font></td>      <td height="23"><font face="Courier New, Courier, mono">cp CURRENT_RELEASE DEFAULT_RELEASE</font></td>
100      <td># Causes the new configuration to use the code that was running in the      <td># Causes the new configuration to use the code that was running in the
101        original installation</td>        original installation</td>
102    </tr>    </tr>
103      <tr>
104        <td height="23"><font face="Courier New, Courier, mono">./configure <em>arch-name</em></font></td>
105        <td># Configure the new SEED disk for architecture <em>arch-name</em>. </td>
106      </tr>
107      <tr>
108        <td height="23"><font face="Courier New, Courier, mono"> source config/fig-user-env.sh <br>
109        </font></td>
110        <td># Set up the environment for using the SEED</td>
111      </tr>
112      <tr>
113        <td height="23"><font face="Courier New, Courier, mono">start-servers <br>
114        </font></td>
115        <td># Start the database server and registration servers</td>
116      </tr>
117      <tr>
118        <td height="23"><font face="Courier New, Courier, mono">init_FIG <br>
119        </font></td>
120        <td># Initialize a new relational database</td>
121      </tr>
122      <tr>
123        <td height="23"><font face="Courier New, Courier, mono">fig load_all</font></td>
124        <td># Load the database from the SEED data files. This may take several hours</td>
125      </tr>
126    </table>
127    <p>At this point, the new SEED copy should be ready to use. You only need to
128      perform the configure, init_FIG, and fig load_all steps once after installing
129      a new copy of the SEED. After a reboot or other clean start of the computer,
130      you will only have to do these steps:</p>
131    <table border="1" bgcolor="#CCCCCC">
132      <tr>
133        <td width="403"><font face="Courier New, Courier, mono">cd ~fig/FIGdisk</font></td>
134        <td width="285">&nbsp;</td>
135      </tr>
136      <tr>
137        <td><font face="Courier New, Courier, mono">bash</font></td>
138        <td>Switch to using the bash shell</td>
139      </tr>
140      <tr>
141        <td height="23"><font face="Courier New, Courier, mono"> source config/fig-user-env.sh <br>
142        </font></td>
143        <td># Set up the environment for using the SEED</td>
144      </tr>
145      <tr>
146        <td height="23"><font face="Courier New, Courier, mono">start-servers <br>
147        </font></td>
148        <td># Start the database server and registration servers</td>
149      </tr>
150  </table>  </table>
151  <p>At this point, the newly-copied FIGdisk can be configured for use. The full  <p>Upon setting up a new computer for running SEED, you should read the full
152    documentation for SEED installation can currently be found at the following    documentation for SEED installation, as it has a number of platform-specific
153      modifications that need to be performed. This document can currently be found
154      at the following
155    location in the SEED Wiki:  </p>    location in the SEED Wiki:  </p>
156  <blockquote>  <blockquote>
157    <p><a href="http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions">      http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions</a></p>    <p><a href="http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions">      http://www-unix.mcs.anl.gov/SEEDWiki/moin.cgi/SeedInstallationInstructions</a></p>
158  </blockquote>  </blockquote>
159  <h1>Running Multiple Copies of the SEED</h1>  <h2>Running Multiple Copies of the SEED</h2>
160    
161  For individual users that use the SEED to support comparative analysis, a single copy is completely  For individual users that use the SEED to support comparative analysis, a single copy is completely
162  adequate.  Adding genomes can usually be done without disrupting normal use, and a very occasional major  adequate.  Adding genomes can usually be done without disrupting normal use, and a very occasional major
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186  Our experience is that anytime a group wishes to share a common production environment,  Our experience is that anytime a group wishes to share a common production environment,
187  this 2-system approach is the way to do it.  this 2-system approach is the way to do it.
188  <br>  <br>
189  <h1>Adding a New Genome to an Existing SEED</h1>  <h2>Adding a New Genome to an Existing SEED</h2>
190  To add a new genome to a running SEED is fairly easy, but there are a  To add a new genome to a running SEED is fairly easy, but there are a
191  number of details that do have to be handled with care.  number of details that do have to be handled with care.
192  <p>  <p>
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438  The <i>add_genome</i> request will add your new genome and queue a computational request that similarities  The <i>add_genome</i> request will add your new genome and queue a computational request that similarities
439  be computed for the protein-encoding genes.  be computed for the protein-encoding genes.
440    
441  <h1>Computing Similarities</h1>  <h2>Computing Similarities</h2>
442    
443  Adding a genome does not automatically get similarities computed for the new genome; it queues the request.  Adding a genome does not automatically get similarities computed for the new genome; it queues the request.
444  To get the similarities actually computed, you need to establish a computational environment on which  To get the similarities actually computed, you need to establish a computational environment on which
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489  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
490  your configuration to exploit these resources.  your configuration to exploit these resources.
491    
492  <h1>Deleting Genomes from a Version of the SEED </h1>  <h2>Deleting Genomes from a Version of the SEED </h2>
493    
494  There are two common instances in which one wishes to delete genomes from a running version of the SEED: one is  There are two common instances in which one wishes to delete genomes from a running version of the SEED: one is
495  when you wish to replace an existing version of a genome (in which case the replacement is viewed as first  when you wish to replace an existing version of a genome (in which case the replacement is viewed as first
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528  <<<< Bob, can you write make_a_SEED??? >>>  <<<< Bob, can you write make_a_SEED??? >>>
529  </pre>  </pre>
530    
531  <h1>Periodic Reintegration of Similarities</h1>  <h2>Periodic Reintegration of Similarities</h2>
532    
533  When the initial SEED was constructed, similarities were computed.  For most similarities of the form  When the initial SEED was constructed, similarities were computed.  For most similarities of the form
534  "Id1 and Id2 are similar", entries were "recorded" for both Id1 and Id2.  This is not always true,  "Id1 and Id2 are similar", entries were "recorded" for both Id1 and Id2.  This is not always true,
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546  </pre>  </pre>
547  The job will probably run for quite a while (perhaps as much as a day or two).  The job will probably run for quite a while (perhaps as much as a day or two).
548    
549  <h1>Computing "Pins" and "Clusters"</h1>  <h2>Computing "Pins" and "Clusters"</h2>
550    
551  The SEED displays potentially significant clusters on prokaryotic chromosomes.  In the  The SEED displays potentially significant clusters on prokaryotic chromosomes.  In the
552  process of finding preserved contiguity, it computes "pins", which are simply a set of genes  process of finding preserved contiguity, it computes "pins", which are simply a set of genes

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