install.html 4.56 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131
<html>
    <head>
        <title>eHive installation and setup</title>
    </head>
<body>

    <center><h1>eHive installation and setup</h1></center>
    <hr width=50% />

    <center><h2>eHive dependencies</h2></center>

    eHive system depends on the following components that you may need to download and install first:
    <ol>
        <li>Perl 5.10 <a href=http://www.perl.org/get.html>or higher</a></li>
        <li>A database engine of your choice. eHive keeps its state in a database, so you will need
            <ol>
                <li>a server installed on the machine where you want to maintain the state of your pipeline(s) and</li>
                <li>clients installed on the machines where the jobs are to be executed.</li>
            </ol>
            At the moment, the following database options are available:
            <ul>
                <li>MySQL 5.1 <a href=http://dev.mysql.com/downloads/>or higher</a></li>
                <li>SQLite 3.6 <a href=http://www.sqlite.org/download.html>or higher</a></li>
                <li>PostgreSQL 9.2 <a href=http://www.postgresql.org/download/>or higher</a></li>
            </ul>
        </li>
        <li>Perl DBI API version 1.6 <a href=http://dbi.perl.org/>or higher</a> --
            Perl database interface that has to include a driver for the database engine of your choice above.
        </li>
        <li>Perl libraries for visualisation (optional but recommended). They can be found on CPAN:
            <ul>
                <li><a href=http://search.cpan.org/~rsavage/GraphViz/lib/GraphViz.pm>GraphViz</a> (needed for generate_graph.pl and the GUI)</li>
                <li><a href=http://search.cpan.org/dist/Chart-Gnuplot/lib/Chart/Gnuplot.pm>Chart::Gnuplot</a> (needed for generate_timeline.pl)</li>
            </ul>
        </li>
        </li>

    </ol>

    <hr width=50% />

    <center><h2>Installing EnsEMBL core and eHive code</h2></center>

<h3>Create a directory for EnsEMBL repositories:</h3>

It is advised to have a dedicated directory where EnsEMBL-related packages will be deployed.
Unlike DBI modules that can be installed system-wide by the system administrator,
you will benefit from full (read+write) access to the EnsEMBL files/directories,
so it is best to install them under your home directory. For example,

<pre>
        $ mkdir $HOME/ensembl_main
</pre>

<h3>Set a variable pointing at this directory:</h3>

<ul>
<li><i>using bash syntax:</i>
<pre>
        $ export ENSEMBL_CVS_ROOT_DIR="$HOME/ensembl_main"<i>
                #
                # (for best results, append this line to your ~/.bashrc or ~/.bash_profile configuration file)</i>
</pre></li>

<li><i>using [t]csh syntax:</i>
<pre>
        $ setenv ENSEMBL_CVS_ROOT_DIR "$HOME/ensembl_main"<i>
                #
                # (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file)</i>
</pre></li>
</ul>

<h3>Change into your EnsEMBL codebase directory:</h3>

<pre>
        $ cd $ENSEMBL_CVS_ROOT_DIR
</pre>

<h3>Check out the EnsEMBL repositories by cloning them from GitHub:</h3>

<ol>
<li><i>EnsEMBL core API:</i>
<pre>
    git clone https://github.com/Ensembl/ensembl.git
</pre></li>
<li><i>eHive code:</i>
<pre>
    git clone https://github.com/Ensembl/ensembl-hive.git
</pre></li>
</ol>

<h3>Add new packages to the PERL5LIB variable:</h3>

<ul>
<li><i>using bash syntax:</i>
<pre>
        $ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
        $ export PERL5LIB=${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules<i>
                #
                # (for best results, append these lines to your ~/.bashrc or ~/.bash_profile configuration file)</i>
</pre></li>

<li><i>using [t]csh syntax:</i>
<pre>
        $ setenv PERL5LIB  ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl/modules
        $ setenv PERL5LIB  ${PERL5LIB}:${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules<i>
                #
                # (for best results, append these lines to your ~/.cshrc or ~/.tcshrc configuration file)</i>
</pre></li>
</ul>

<h3>Add eHive scripts' path to the PATH variable (optional but useful) :</h3>

<ul>
<li><i>using bash syntax:</i>
<pre>
        $ export PATH=$PATH:$ENSEMBL_CVS_ROOT_DIR/ensembl-hive/scripts<i>
                #
                # (for best results, append this line to your ~/.bashrc or ~/.bash_profile configuration file)</i>
</pre></li>

<li><i>using [t]csh syntax:</i>
<pre>
        $ set path = ( $path ${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/scripts )<i>
                #
                # (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file)</i>
</pre></li>
</ul>

</body>
</html>