Changeset 1236


Ignore:
Timestamp:
Aug 31, 2010, 9:33:04 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Fixed layout issues in trac presentation.

File:
1 edited

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  • plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

    r1226 r1236  
    1 ----------------------------------------------------------------------
    2 {{{
    3 Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg
    4 Copyright (C) 2009 Jari Häkkinen, Martin Svensson
    5 
    6 This file is part of Illumina plug-in package for BASE.
    7 Available at http://baseplugins.thep.lu.se/
    8 BASE main site: http://base.thep.lu.se/
    9 
    10 This is free software; you can redistribute it and/or
    11 modify it under the terms of the GNU General Public License
    12 as published by the Free Software Foundation; either version 3
    13 of the License, or (at your option) any later version.
    14 
    15 The software is distributed in the hope that it will be useful,
    16 but WITHOUT ANY WARRANTY; without even the implied warranty of
    17 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    18 GNU General Public License for more details.
    19 
    20 You should have received a copy of the GNU General Public License
    21 along with BASE. If not, see <http://www.gnu.org/licenses/>.
    22 }}}
    23 ----------------------------------------------------------------------
    24 
    25 == How to install or upgrade the Illumina plug-ins package for BASE. ==
     1= How to install or upgrade the Illumina plug-ins package for BASE. =
    262
    273
    … …  
    3814    If you have job agents that are running from another location, you must also
    3915    copy the jar file to a location the job agents has access to.   
    40  4. From the ''config'' directory, copy:
     16 4. From the ''config'' directory, copy ('''Notice: If you have job
     17    agents running from another location, copy the configuration files
     18    to a location the job agents has access to.'''):
    4119     * ''illumina-extended-properties.xml'' to <basedir>''/www/WEB-INF/classes/extended-properties/''
    42      * ''illumina-raw-data-types-xml'' to <basedir>''/www/WEB-INF/classes/raw-data-types/''[[BR]]
    43        '''Notice: If you have job agents that are running from another location, copy the
    44        configuration files to a location the job agents has access to.'''   
     20     * ''illumina-raw-data-types-xml'' to <basedir>''/www/WEB-INF/classes/raw-data-types/''
    4521 5. Update the database with Illumina-specific tables and columns by running the
    4622    ''updatedb.sh'' script, located in the <basedir>''/bin'' directory.
    … …  
    6541    program to create a scanner and/or software entry.
    6642 13. Finish the job registration and wait for the plug-in to finish.
    67  14. If the extension auto-installation is disabled a manual scan is necessary to detect/register the new illumina-extensions.
    68    Click on menu: ''Extensions -> Manual scan...''
     43 14. If the extension auto-installation is disabled a manual scan is
     44    necessary to detect/register the new illumina-extensions; Click on
     45    menu: ''Extensions -> Manual scan...''
    6946 15. Done. The Illumina plug-ins are now installed. You can now restart any job
    7047    agents as well.
    … …  
    8562'''Notice: you may have to configure the JAR path manually for each job agent.'''
    8663
     64
    8765== Upgrade ==
    8866
    … …  
    9068already installed Illumina package.
    9169 1. Do the step 1-3 as described in the installation instructions.
    92  2. Then proceed with step 4. '''Caution:''' ''Any changes in the files on the local server must be transferred
    93   to the new configuration-files before they are copied.'' Copying the new files will overwrite the existing files.
     70 2. Then proceed with step 4. [[br]]
     71    '''Caution:''' ''Any changes in the files on the local server must
     72    be transferred to the new configuration-files before they are
     73    copied.'' Copying the new files will overwrite the existing
     74    files.
    9475 3. Do step 5-6 as described.
    9576 4. Step 7-9 are optional and only needed if the new release contains plugins or changed/new plugin configurations
    9677    that you want to install. [[BR]]
    97     '''Notice1:''' Already installed plugins do not need to be re-installed(unless the jar-path has been changed), but updated configurations do.[[BR]]
    98     '''Notice2:''' If the existing configuration is not first removed  you will end up with two configurations with the same name.
    99     '''Notice3:''' Upgrading from 1.3.x or less require you to run the installation wizard even for the installed plugins to update their jar-path.
     78    '''Notice 1:''' Already installed plugins do not need to be
     79    re-installed(unless the jar-path has been changed), but updated
     80    configurations do.[[BR]]
     81    '''Notice 2:''' If the existing configuration is not first removed
     82    you will end up with two configurations with the same name. [[br]]
     83    '''Notice 3:''' Upgrading from 1.3.x or less require you to run
     84    the installation wizard even for the installed plugins to update
     85    their jar-path.
    10086 5. Step 10-13 are also optional and only necessary when the release comes with new Illumina variants that you want to create.
    10187 6. Do step 14 to update the extensions.
    10288 7. Done. The Illumina package is now updated. You can restart any job-agents as well.
     89
     90----------------------------------------------------------------------
     91{{{
     92Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg
     93Copyright (C) 2009 Jari Häkkinen, Martin Svensson
     94Copyright (C) 2010 Jari Häkkinen, Nicklas Nordborg
     95
     96This file is part of Illumina plug-in package for BASE.
     97Available at http://baseplugins.thep.lu.se/
     98BASE main site: http://base.thep.lu.se/
     99
     100This is free software; you can redistribute it and/or
     101modify it under the terms of the GNU General Public License
     102as published by the Free Software Foundation; either version 3
     103of the License, or (at your option) any later version.
     104
     105The software is distributed in the hope that it will be useful,
     106but WITHOUT ANY WARRANTY; without even the implied warranty of
     107MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     108GNU General Public License for more details.
     109
     110You should have received a copy of the GNU General Public License
     111along with BASE. If not, see <http://www.gnu.org/licenses/>.
     112}}}
     113----------------------------------------------------------------------
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