====== Installation of ReadSeq 2.1.30 ======

===== Additional libraries ===== 

Java, already installed.

===== Procedure =====

Here is the procdure to install:

  * ReadSeq is distributed as a JAR archive, ready to run. You create a folder under ''/home/bioubuntu'' to put it in, you download the JAR file and you move this folder under ''/opt/bio/sources''.

<code bash>
% mkdir readseq-2.1.30
% cd readseq-2.1.30
% wget http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq.jar
$ cd .. & sudo mv readseq-2.1.30 /opt/bio/sources
</code>

  * This folder should belong to ''root'' and its permissions should be set to ''755''.

<code bash>
% sudo chown -R root:root /opt/bio/sources/readseq-2.1.30
% sudo chmod 755 /opt/bio/sources/readseq-2.1.30
</code>

  * Once you are in ''/opt/bio/sources/readseq-2.1.30'', you need to create two small scripts to help its use:
<code bash>
% sudo touch readseq
% sudo touch readseq_gui
</code>

  * for ''readseq'', put the following code:
<code>
#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.30/readseq.jar run
</code>

  * For ''readseq_gui'', put the following code:
<code>
#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.30/readseq.jar app
</code>


  * To make this scripts runnable and to make them available to all:
<code bash>
% sudo chmod ugo+x readseq
% sudo ln -s /opt/bio/sources/readseq-2.1.30/readseq /usr/local/bin/readseq
% sudo chmod ugo+x readseq_gui
% sudo ln -s /opt/bio/sources/readseq-2.1.30/readseq_gui /usr/local/bin/readseq_gui
</code>

  * To add ReadSeq in the Impilo > General purpose tools:
    * More to come...

  * To use readseq_gui from the command line:

<code bash>
% readseq_gui
</code>