Java, already installed.

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.

% 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

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

% sudo chown -R root:root /opt/bio/sources/readseq-2.1.30
% sudo chmod 755 /opt/bio/sources/readseq-2.1.30

• Once you are in /opt/bio/sources/readseq-2.1.30, you need to create two small scripts to help its use:

% sudo touch readseq
% sudo touch readseq_gui

• for readseq, put the following code:

#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.30/readseq.jar run

• For readseq_gui, put the following code:

#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.30/readseq.jar app

• To make this scripts runnable and to make them available to all:

% 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

• To add ReadSeq in the Impilo > General purpose tools:
  • More to come…

• To use readseq_gui from the command line:

% readseq_gui