Commit 78bad716 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Merge branch 'version/2.2'

* version/2.2:
  Included parts of Fergal's text in the docs
  Added some whitespace around <hr> elements
parents 385c9378 735ab349
......@@ -32,6 +32,8 @@ th, td { font-size: 0.8em; }
body.ie6 th, body.ie6 td { font-size: 13px; }
hr { margin-top:40px; margin-bottom:20px }
/*----------------------------------------------------------------------
New classes defined for the eHive documents
----------------------------------------------------------------------*/
......
......@@ -43,14 +43,41 @@
<h3>Check out the repository by cloning it from GitHub:</h3>
<p>
All eHive pipelines will require the ensembl-hive repository, which can be found on
<a href="https://github.com/Ensembl/ensembl-hive">GitHub</a>. As such it is assumed that <a href="http://git-scm.com/">Git</a> is
installed on your system, if not follow the instructions <a href="https://help.github.com/articles/set-up-git/">here</a>
</p>
<p>
To download the repository, move to a suitable directory and run the following on the
command line:
</p>
<pre>
$ git clone https://github.com/Ensembl/ensembl-hive.git
git clone https://github.com/Ensembl/ensembl-hive.git
</pre>
<p>
This will create ensembl-hive directory with all the code and documentation.
This will create ensembl-hive directory with all the code and documentation.<br/>
If you cd into the ensembl-hive directory and do an ls you should see something like the
following:
</p>
<pre>
ls
Changelog docs hive_config.json modules README.md scripts sql t
</pre>
The major directories here are:
<dl>
<dt>modules</dt>
<dd>This contains all the eHive modules, which are written in Perl</dd>
<dt>scripts</dt>
<dd>Has various scripts that are key to initialising, running and debugging the pipeline</dd>
<dt>sql</dt>
<dd>Contains sql used to build a standard pipeline database</dd>
</dl>
<h3>Optional configuration of the system:</h3>
......@@ -62,14 +89,14 @@ to your <code>$PATH</code> variable to make it easier to run beekeeper.pl and ot
<ul>
<li><i>using bash syntax:</i>
<pre>
$ export PATH=$PATH:$ENSEMBL_CVS_ROOT_DIR/ensembl-hive/scripts<i>
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>
set path = ( $path ${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/scripts )<i>
#
# (for best results, append this line to your ~/.cshrc or ~/.tcshrc configuration file)</i>
</pre></li>
......@@ -83,16 +110,16 @@ you may find it convenient to add "ensembl-hive/modules" to your <code>$PERL5LIB
<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>
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>
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>
......
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