Changeset 3113


Ignore:
Timestamp:
Feb 7, 2007, 2:13:41 AM (15 years ago)
Author:
Jari Häkkinen
Message:

Updated installation document.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/installation.html

    r3056 r3113  
    44    $Id$
    55
    6     Copyright (C) 2005-2006 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
     6    Copyright (C) 2005-2007 Jari Häkkinen, Nicklas Nordborg, Gregory Vincic
    77
    88    This file is part of BASE - BioArray Software Environment.
     
    6060  <b>Created by:</b> Nicklas, Jari<br>
    6161  <b>Last updated:</b> $Date$<br>
    62   <b>Copyright &copy;</b> 2005-2006 The respective authors. All rights reserved.
     62  <b>Copyright &copy;</b> 2005-2007 The respective authors. All rights reserved.
    6363  </p>
    6464
     
    9090  <p>
    9191    b) PostgreSQL<br>
    92     PostgreSQL 8.0 seems to be working very well. Actually sometimes even better
    93     than with MySQL. If you want to use Postgres instead of MySQL you will have to edit
    94     your <code>base.config</code> file. Uncomment the settings for Postgres and comment
    95     out the settings for MySQL.
     92    PostgreSQL 8.0 seems to be working very well. If you want to use
     93    Postgres instead of MySQL you will have to edit
     94    your <code>base.config</code> file. Uncomment the settings for
     95    Postgres and comment out the settings for MySQL.
    9696  </li>
    9797
     
    120120  <p>
    121121  If you choose to download the binary package, skip to the next
    122   item. The rest of us, read on and compile BASE 2. If you
    123   downloaded a source distribution, unpack the downloaded file <tt>tar zxpf
    124   base-...src.tar.gz</tt>, or you may have performed a subversion checkout.
    125   Change to the 'root' base2 directory, and issue <tt>ant
    126   package.bin</tt>. This will create a binary package in the base2 root
    127   directory. Unpack this new package (outside of the source file
    128   hierarchy), and from now on the instructions are the same however
    129   you got the binary.
     122  item. The rest of us, read on and compile BASE 2. If you downloaded
     123  a source distribution, unpack the downloaded file <tt>tar zxpf
     124  base-...src.tar.gz</tt>, or you may have performed a subversion
     125  checkout.  Change to the 'root' base2 directory, and issue <tt>ant
     126  package.bin</tt>. This will create a binary package in the base2
     127  'root' directory. Unpack this new package (outside of the source
     128  file hierarchy), and from now on the instructions are the same
     129  irrespective where you got the binary package.
    130130  </p>
    131131
     
    137137    accomplish this is available in the
    138138    <a href=development/index.html#running>developer documentation
    139     pages</a>. The rest of the instructions here apply also for this
    140     use case.</i>
     139    pages</a>. When you return back after compiling in the subversion
     140    tree you can follow the instruction here (with obvious changes to
     141    paths).</i>
    141142  </p>
    142143  </li>
     
    172173 
    173174  <p>
    174     The <code>base-2.0/misc/sql/createdb.mysql.sql</code> file
     175    The <code>/path_to_base/misc/sql/createdb.mysql.sql</code> file
    175176    contains the above statements and can be used by the <code>mysql</code>
    176177    command-line tool (remember to edit the <tt>user</tt>,
     
    201202  </p>
    202203  <p>
    203     The <code>base-2.0/misc/sql/createdb.postgresql.sql</code> file
     204    The <code>/path_to_base/misc/sql/createdb.postgresql.sql</code> file
    204205    contains the above statements and can be used by the <code>psql</code>
    205206    command-line tool:
     
    227228      <li>
    228229        Configure BASE, in
    229         <code>base-2.0/www/WEB-INF/classes/base.config</code> do:
     230        <code>/path_to_base/www/WEB-INF/classes/base.config</code> do:
    230231        <ol type=a>
    231232          <li>
     
    246247      <li>
    247248        Modify extended properties as needed through
    248         file <code>base-2.0/www/WEB-INF/classes/extended-properties.xml</code>. This
     249        file <code>/path_to_base/www/WEB-INF/classes/extended-properties.xml</code>. This
    249250        is not strictly needed but may be preferred. There is a
    250251        administrator <a href=admin/extended-properties.html>document
     
    258259    <i>BASE</i> (database initialization)<br>
    259260    Change directory to
    260     <code>base-2.0/bin</code> and run <code>initdb.sh</code> as
     261    <code>/path_to_base/bin</code> and run <code>initdb.sh</code> as
    261262<pre>
    262263    ./initdb.sh password
     
    277278    available from <a
    278279    href=http://jakarta.apache.org/tomcat/>http://jakarta.apache.org/tomcat/</a>.
    279     We are now recommending everyone to run a late 5.5 release since
    280     the trick described in <a
    281     href=http://lev.thep.lu.se/trac/base/browser/trunk/doc/tomcat_with_java_1.5.txt>doc/tomcat_with_java_1.5.txt</a> is not needed anymore.
    282     [<i>We have previously tested BASE with tomcat releases 5.0.30 and
    283     5.5.7. However, these versions use a built in Java 1.4 compiler,
    284     to make it work with Java 1.5 read and follow the instructions in
    285     <a
    286     href=http://lev.thep.lu.se/trac/base/browser/trunk/doc/tomcat_with_java_1.5.txt>doc/tomcat_with_java_1.5.txt</a>
    287     and, consequently, download Apache ANT from <a
    288     href=http://ant.apache.org/>http://ant.apache.org/</a>.</i>]
    289   </p>
    290   </li>
    291 
    292 
    293   </p>
    294  
    295   <p>
    296     You MUST also make sure that Tomcat uses the SERVER mode of the Java
     280  </p>
     281  <p>
     282    You MUST make sure that Tomcat uses the SERVER mode of the Java
    297283    run time engine (see <a href="http://lev.thep.lu.se/trac/base/ticket/99">ticket #99</a>).
    298284    On Linux you do this by setting the environment variable:
     
    312298  href="http://www.chemaxon.com/jchem/doc/admin/tomcat.html">http://www.chemaxon.com/jchem/doc/admin/tomcat.html</a>.
    313299  </p>
    314 
     300  </li>
    315301  <li>
    316302  <p>
    317303    <i>BASE/tomcat</i> <br>
    318304    Either move the
    319     <code>base-2.0/www</code> directory to the tomcat webapps
     305    <code>/path_to_base/www</code> directory to the tomcat webapps
    320306    directory or create a symbolic link from the tomcat webapps
    321     directory to the <code>www</code> directory (<code>ln -s /path/to/base2/www
    322     base2</code>). Start/restart tomcat, and try http://hostname/base2
     307    directory to the <code>www</code> directory (<code>ln -s /path_to_base/www
     308    base2</code>). Start/restart tomcat, and try http://hostname:8080/base2
    323309    (replace base2 with whatever you use in your tomcat webapps
    324310    directory) in your favourite browser, you should expect to see the
    325311    BASE login page after a few seconds.
    326312  </p>
    327 
    328   <p>
    329     In some cases when redoing the installation, the behaviour of
    330     tomcat/apache/base may seem strange. This may be due to tomcat's
    331     caching of the applications installed. The easiest way to test
    332     whether the caching creates problems is to simply delete the cached
    333     files. On SuSE 9.3 this is done by (with tomcat5)
    334   </p>
    335  
    336 <pre class="code">
    337   rm -rf /etc/tomcat5/base/Catalina/localhost
    338   rm -rf ~tomcat/work/Catalina
    339 </pre>
    340 
    341313  </li>
    342314
     
    344316  <p>
    345317    <i>BASE, apache and apache/tomcat connector</i>
    346     <br> This step is optional. If you want run the tomcat server
     318    <br> <strong>This step is optional</strong>. If you want run the
     319    tomcat server
    347320    through the apache web server, you need to install the apache
    348321    version 2 web server, available from <a
     
    351324    href="http://jakarta.apache.org/tomcat/connectors-doc/index.html">http://jakarta.apache.org/tomcat/connectors-doc/index.html</a>.
    352325    So, we got you there;-) To be honest, this item is not really well
    353     documented yet since we use SuSE 9.3 on our demo/test server, and
     326    documented since we use SuSE 9.3 on our demo/test server, and
    354327    apache/tomcat/mod_jk comes pre-installed. What you need to do is:
    355328    <ol type=a>
     
    404377
    405378<p>
    406 <i> Upgrading BASE to versions below 2.2 may not be safe on a PostgreSQL database due to a bug in
    407 Hibernate. The problem is reported to Hibernate developers. There now exists
    408 a workaround for this problem. Read more about it on the
    409 <a href="http://base.thep.lu.se/wiki/UpgradePostgres">Upgrading a Postgres database</i>
    410 page. Note! This bug has been fixed in the Hibernate version which is shipped with
    411 BASE 2.2 and above.
     379<i> Note to PostgreSQL users: Upgrading BASE to versions earlier than
     380v2.2 is not be safe with an PostgreSQL database engine due to a bug in
     381Hibernate. The problem is reported to Hibernate developers. There now
     382exists a workaround for this problem. Read more about it on the
     383<a href="http://base.thep.lu.se/wiki/UpgradePostgres">Upgrading a
     384Postgres database</a> page. Note! The Hibernate bug has been fixed in
     385the Hibernate package shipped with BASE 2.2 and above. </i>
    412386</p>
    413387
     
    423397  <li>
    424398  <p>
    425   Rename your current BASE 2 installation <tt>mv base-2.0 base-2.0_old</tt>
     399  Rename your current BASE 2 installation <tt>mv /path_to_base
     400  /path_to_base_old</tt>
    426401  </p>
    427402  </li>
     
    434409  BASE 2</a> and unpack the downloaded file, i.e. <tt>tar zxpf
    435410  base-...tar.gz</tt>. If you prefer to have the bleeding edge
    436   version of BASE 2.0, perform a checkout of the source from the
     411  version of BASE 2, perform a checkout of the source from the
    437412  subversion repository (subversion checkout instructions at <a
    438   href=http://lev.thep.lu.se/trac/base/wiki>BASE 2.0 trac site</a>).
     413  href=http://base.thep.lu.se>BASE 2 trac site</a>).
    439414  </p>
    440415
    441416  <p>
    442417  If you choose to download the binary package, skip to the next
    443   item. The rest of us, read on and compile BASE 2. If you
    444   downloaded a source distribution, unpack the downloaded file <tt>tar zxpf
    445   base-...src.tar.gz</tt>, or you may have performed a subversion checkout.
    446   Change to the 'root' base2 directory, and issue <tt>ant
    447   package.bin</tt>. This will create a binary package in the base2 root
    448   directory. Unpack this new package (outside of the source file
    449   hierarchy), and from now on the instructions are the same however
    450   you got the binary.
    451   </p>
    452   </li>
    453 
    454   <li>
    455   <p>
    456   You need to transfer settings made from the old installation
    457   to the new. This is most easily done by comparing the configuration file
    458   (<tt>base-2.0/www/WEB-INF/classes/base.config</tt>) between the
    459   new and the old install (usually fields db.username, db.password,
    460   userfiles).
     418  item. The rest of us, read on and compile BASE 2. If you downloaded
     419  a source distribution, unpack the downloaded file <tt>tar zxpf
     420  base-...src.tar.gz</tt>, or you may have performed a subversion
     421  checkout.  Change to the 'root' BASE 2 directory, and issue <tt>ant
     422  package.bin</tt>. This will create a binary package in the BASE 2
     423  'root' directory. Unpack this new package (outside of the source
     424  file hierarchy), and from now on the instructions are the same
     425  irrespective where you got the binary package.
     426  </p>
     427  </li>
     428
     429  <li>
     430  <p>
     431  You need to transfer settings made from the old installation to the
     432  new. This is most easily done by comparing the configuration file
     433  (<tt>/path_to_base/www/WEB-INF/classes/base.config</tt>) between the
     434  new and the old install (usually fields db.username, db.password,
     435  userfiles need to be transferred).
    461436  </p>
    462437  <p>
     
    469444  <li>
    470445  <p>
    471   <i> Note, this is not safe on a PostgreSQL database due to a bug in
    472   Hibernate. The problem is reported to Hibernate developers.</i> <br>
    473   It is recommended that you perform an update of your database.
    474   Running the update scripts are not always necessary, but the update
    475   is safe to perform even in cases when it is not needed. Change
    476   directory to <tt>/path/to/base-2.0/bin/</tt> and issue: <br>
     446  It is recommended that you also perform an update of your
     447  database.  Running the update scripts are not always necessary when
     448  upgrading BASE 2, but the update is safe to perform even in cases
     449  when it is not needed. Change directory
     450  to <tt>/path_to_base/bin/</tt> and issue: <br>
    477451  <tt>sh ./updatedb.sh <font color=#00ccc0><i>password</i></font> ;
    478452  sh ./updateindexes.sh <font
     
    485459  <li>
    486460  <p>
    487   As tomcat user, remove cached files and directories. Something like this
     461  As tomcat user, remove cached files and directories. Do something
     462  like this
    488463<pre>
    489464cd /usr/share/apache-tomcat-5.5.15/
     
    507482</ol>
    508483
    509 <h2><a name=migration>BASE 1.2 to 2.0 data migration instructions</a></h2>
     484<h2><a name=migration>BASE 1.2 to 2.2 data migration instructions</a></h2>
    510485
    511486<p>
     
    515490supplied as is and usage is done at your risk. We are committed to
    516491solve migration problems at the level of transferring data from BASE
    517 1.2 to 2.0.x, but cannot resolve data loss issues due to imperfect
    518 migration in a running BASE 2.0.x server. When you start the migration
    519 tool you are required to pass parameter "disclaimer_understood" to the
     4921.2 to 2.2.x, but cannot resolve data loss issues in a running BASE 2
     493server due to imperfect migration. When you start the migration tool
     494you are required to pass parameter "disclaimer_understood" to the
    520495migrate_from_1.2.sh script. Remember to check that the migration
    521496performed well before you decide to delete your 1.2 installation.
     
    523498
    524499<p>
    525   Verify that your BASE 2.0 installation is up and running before
     500  Verify that your BASE 2 installation is up and running before
    526501  attempting migration. Preferably try to login using the root user
    527502  through the web interface.
     
    560535  <p>
    561536  Change settings in the file
    562   <code>base-2.0/dist/www/WEB-INF/classes/migrate.properties</code>.
     537  <code>/path_to_base/dist/www/WEB-INF/classes/migrate.properties</code>.
    563538  The available options are commented:
    564539  <ol type=a>
     
    575550      Set the <code>pluginDir</code> to point to the directory
    576551      where your BASE 1 plug-ins are installed. The default is
    577       <code>/usr/loca/base/plugins</code>.
     552      <code>/usr/local/base/plugins</code>.
    578553    </li>
    579554    <li>
     
    595570    Run migration utility:
    596571<pre class="code">
    597   cd base-2.0/dist/bin
     572  cd /path_to_base/dist/bin
    598573  ./migrate_from_1.2.sh
    599574</pre>
Note: See TracChangeset for help on using the changeset viewer.