Commit 7eb79753 authored by Leo Gordon's avatar Leo Gordon
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adding reformatted install.html and README.md links to HTML documents (relying...

adding reformatted install.html and README.md links to HTML documents (relying on htmlpreview functionality)
parent 609fcc7f
EnsEMBL Hive
============
eHive
=====
EnsEMBL Hive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.
eHive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.
The name "Hive" comes from the way pipelines are processed by a swarm of autonomous agents.
The name comes from the way pipelines are processed by a swarm of autonomous agents.
Blackboard, Jobs and Workers
----------------------------
......@@ -28,7 +28,7 @@ However in some sense an Analysis also acts as a "container" for them.
PipeConfig file defines Analyses and dependency rules of the pipeline
---------------------------------------------------------------------
Hive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface.
eHive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface.
A PipeConfig file defines the stucture of the pipeline, which is a graph whose nodes are Analyses
(with their code, parameters and resource requirements) and edges are various dependency rules:
* Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses
......@@ -44,12 +44,17 @@ There are also other parameters of Analyses that control, for example:
* what should be autimatically done with a Job if it needs more memory/time,
etc.
Available documentation
-----------------------
* eHive dependencies, installation and setup [(on GitHub)](http://htmlpreview.github.io/?https://github.com/Ensembl/ensembl-hive/blob/master/docs/install.html) [(local)](docs/install.html)
* eHive database schema [(on GitHub)](http://htmlpreview.github.io/?https://github.com/Ensembl/ensembl-hive/blob/master/docs/hive_schema.html) [(local)](docs/hive_schema.html)
Contact us (mailing list)
-------------------------
EnsEMBL Hive was originally conceived and used within EnsEMBL Compara group
eHive was originally conceived and used within EnsEMBL Compara group
for running Comparative Genomics pipelines, but since then it has been separated
into a separate software tool and is used in many projects both in Genome Campus, Cambridge and outside.
There is a Hive users' mailing list for questions, suggestions, discussions and announcements.
There is eHive users' mailing list for questions, suggestions, discussions and announcements.
To subscribe to it please visit:
http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users
......
<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>
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