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ensembl-gh-mirror
ensembl-hive
Commits
807bb008
Commit
807bb008
authored
Jun 09, 2017
by
Leo Gordon
Browse files
tweaked the installation docs to make automatic use of cpanfile
parent
1030f99a
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docs/install.html
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807bb008
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@@ -13,6 +13,7 @@
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>
...
...
@@ -27,14 +28,19 @@
<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>
GraphViz visualization package (includes "dot" executable and libraries used by the Perl dependencies).
<ol>
<li>
Check in your terminal that you have "dot" installed
</li>
<li>
If not, visit
<a
href=
http://graphviz.org/
>
graphviz.org
</a>
to download it
</li>
</ol>
</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>
cpanm -- a handy utility to recursively install Perl dependencies.
<ol>
<li>
Check in your terminal that you have "cpanm" installed
</li>
<li>
If not, visit
<a
href=
https://cpanmin.us
>
cpanmin.us
</a>
to download it (just read and follow the instructions in the header of the script)
</li>
</ol>
</li>
</ol>
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@@ -81,7 +87,22 @@ The major directories here are:
</dl>
<h3>
Optional configuration of the system:
</h3>
<hr
width=
50%
/>
<center><h2>
Use cpanm to recursively install the Perl dependencies declared in ensembl-hive/cpanfile
</h2></center>
<pre>
cd ensembl-hive
cpanm --installdeps .
</pre>
<p>
If installation of either DBD::mysql or DBD::Pg fails, check that the corresponding database system (MySQL or PostgreSQL) was installed correctly.
</p>
<hr
width=
50%
/>
<center><h2>
Optional configuration of the system:
</h2></center>
<p>
You may find it convenient (although it is not necessary) to add "ensembl-hive/scripts"
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