Changeset 286


Ignore:
Timestamp:
Jul 5, 2013, 1:13:47 PM (6 years ago)
Author:
david.vanenckevort@…
Message:

Updated documentation.

Location:
trunk/doc
Files:
1 deleted
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/INSTALL

    r263 r286  
     1= FGWeb Installation Manual =
    12Copyright 2001-2010 Sacha van Hijum
     3
    24Copyright 2010 Netherlands Bioinformatics Centre
     5
    36This software is co-developed by the Netherlands Bioinformatics Centre
    47
     
    1619
    1720You should have received a copy of the GNU Affero General Public
    18 License along with FG Web.  If not, see <http://www.gnu.org/licenses/>.
     21License along with FG Web. If not, see <http://www.gnu.org/licenses/>.
    1922
    20 INSTALLATION
    21 If you check out from subversion, the modules are separated from the framework.
    22 The files from each module you pick must be copied into the fgweb root
    23 directory.
    24 If you downloaded the compressed tar archives you extract the files in
    25 a common installation directory (e.g. /opt/fgweb).
     23== INSTALLATION ==
    2624
    27 COMMON
    28 1. Place the files from the distribution in a common directory (/opt/fgweb).
    29 2. Set the following environment variables:
    30    * PERL5LIB, include /opt/fgweb/main/src/lib/perl (e.g. export PERL5LIB=${PERL5LIB}:/opt/fgweb/main/src/lib/perl)
    31    * FGWEB_DIR point to the installation directory (e.g. export FGWEB_DIR=/opt/fgweb)
    32    In most systems you can configure the variables globally with /etc/environment
    33 3. Review the included global_info.inc.php and make changes where necessary
     25  1.    Copy the files from main/src to your web server's document root
     26  2.    Copy the modules you need from modules/ into the web server's document root. For the !SysAdmin module only the code in modules/sysadmin/src should be copied into a sysadmin directory in the web root.
     27  3.    Copy the files from php-lib/src to your PHP include path or add this directory to the PHP include path
     28  4.    Download and install the software listed in REQUIRED SOFTWARE
     29  5.    Configure the software. Review the following files php-lib/src/FGWeb/Config/Db.php, main/src/fgweb_cgi.inc.php, main/src/lib/php/global_info.inc.php
    3430
    35 NOTE
    36 1. Currently AppArmor or SELinux is not supported, make sure you disable them.
    37    Contributions to support them are welcome.
    38 2. Apache needs to have read access to all files, and write access to the
    39    work directory.
    40 
    41 APACHE & PHP CONFIGURATION
    42 1. Review /etc/php.ini and adjust the following settings if necessary.
     31=== APACHE & PHP CONFIGURATION ===
     32 1. Review /etc/php.ini and adjust the following settings if necessary.
     33{{{
    4334[PHP]
    4435register_long_arrays = On
     
    4738upload_max_filesize = 75M
    4839default_socket_timeout = 120
     40}}}
     41 2. Create a virtual host for fgweb.
     42 3. Restart Apache to make these changes active.
     43 4. Go to http://localhost/html/admin/index.php to setup the initial user database.
    4944
    50 2. Create a virtual host for fgweb.
    51 See the included apache.conf in the doc directory for an example.
    52 
    53 3. Restart Apache to make these changes active.
    54 
    55 4. Go to http://localhost/html/admin/index.php to setup the initial user database.
    56 
    57 REQUIRED SOFTWARE
    58 1. Make sure the following software is installed:
     45=== REQUIRED SOFTWARE ===
     46Make sure the following software is installed:
    5947   * Perl 5 with:
    6048     * Config::IniFiles
     
    7159     * Smarty
    7260
    73 For RedHat the EPEL repository is required, see http://fedoraproject.org/wiki/EPEL for installation instructions.
    74 On RedHat:
     61==== Red Hat ====
     62For !RedHat the EPEL repository is required, see [http://fedoraproject.org/wiki/EPEL] for installation instructions.
    7563
     64{{{
    7665yum install perl-SOAP-Lite perl-GD perl-IO-All perl-Data-Dump perl-Config-IniFiles perl-Devel-Cover perl-Test-Class \
    7766  php-pear-Log php-Smarty
     67}}}
    7868
    79 On Debian / Ubuntu:
     69==== Debian / Ubuntu ====
    8070
     71{{{
    8172apt-get install libsoap-lite-perl libgd-graph-perl libconfig-inifiles-perl libdevel-cover-perl libtest-class-perl \
    8273 php-log smarty3 phpunit
     74}}}
    8375
    84 On Mac OS X:
    85  Download XAMPP (http://www.apachefriends.org/en/xampp-macosx.html) and Smarty (http://www.smarty.net)
    86  Smarty can be placed in the fgweb/lib directory, make sure to include it in your apache php configuration.
     76==== On Mac OS X ====
     77Download [http://www.apachefriends.org/en/xampp-macosx.html XAMPP] and [http://www.smarty.net Smarty]
    8778
    88 ADDITIONAL TOOLS
     79Smarty can be placed in the /Applications/XAMPP/xamppfiles/lib/php/ or include the installation directory in your PHP include path
     80
     81== ADDITIONAL TOOLS ==
    8982Depending on your usage you want to install one or more of the following tools
    9083in the tools directory. Each tool has it's own directory, make sure you
     
    9285that the installation path matches what you specified there.
    9386
    94 Blast                   http://blast.ncbi.nlm.nih.gov/Blast.cgi
    95 Blat                    http://www.kentinformatics.com/products.html
    96 Clustalw                http://www.clustal.org/
    97 Fasta                   http://faculty.virginia.edu/wrpearson/fasta/
    98 HMMER                   http://hmmer.janelia.org/
    99 inparanoid              http://inparanoid.sbc.su.se/cgi-bin/index.cgi
    100 primer3                 http://jura.wi.mit.edu/rozen
    101 oligotm                 http://jura.wi.mit.edu/rozen
    102 R/hdarray.R             http://molgen51.biol.rug.nl/cybert/help/index.html
    103 transterm               http://www.cs.jhu.edu/~genomics/TransTerm/transterm.html
    104 transterm_hp    http://transterm.cbcb.umd.edu/
     87 * [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast]
     88 * [http://www.kentinformatics.com/products.html Blat]
     89 * [http://www.clustal.org/ Clustalw]
     90 * [http://faculty.virginia.edu/wrpearson/fasta/ Fasta]
     91 * [http://hmmer.janelia.org/ HMMER]
     92 * [http://inparanoid.sbc.su.se/cgi-bin/index.cgi inparanoid]
     93 * [http://jura.wi.mit.edu/rozen primer3]
     94 * [http://jura.wi.mit.edu/rozen oligotm]
     95 * [http://molgen51.biol.rug.nl/cybert/help/index.html R/hdarray.R]
     96 * [http://www.cs.jhu.edu/~genomics/TransTerm/transterm.html transterm]
     97 * [http://transterm.cbcb.umd.edu/ transterm_hp]
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