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ensembl-gh-mirror
ensembl-hive
Commits
70c33b3c
Commit
70c33b3c
authored
Sep 01, 2014
by
Matthieu Muffato
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Updated the installation guide for 2.0
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docs/install.html
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70c33b3c
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@@ -39,57 +39,46 @@
<hr
width=
50%
/>
<center><h2>
Installing
EnsEMBL core and
eHive code
</h2></center>
<center><h2>
Installing 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,
<h3>
Check out the repository by cloning it from GitHub:
</h3>
<pre>
$
mkdir $HOME/ensembl_main
$
git clone https://github.com/Ensembl/ensembl-hive.git
</pre>
<h3>
Set a variable pointing at this directory:
</h3>
<p>
This will create ensembl-hive directory with all the code and documentation.
</p>
<h3>
Optional configuration of the system:
</h3>
<p>
You may find it convenient (although it is not necessary) to add "ensembl-hive/scripts"
to your
<code>
$PATH
</code>
variable to make it easier to run beekeeper.pl and other useful Hive scripts.
</p>
<ul>
<li><i>
using bash syntax:
</i>
<pre>
$ export ENSEMBL_CVS_ROOT_DIR
="$HOME
/ensembl
_main"
<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
env
ENSEMBL_CVS_ROOT_DIR
"$HOME
/ensembl
_main"
<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>
</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>
<p>
Also, if you are developing the code and not just running ready pipelines,
you may find it convenient to add "ensembl-hive/modules" to your
<code>
$PERL5LIB
</code>
variable.
</p>
<ul>
<li><i>
using bash syntax:
</i>
...
...
@@ -109,23 +98,5 @@ so it is best to install them under your home directory. For example,
</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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