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JBiclustGE-GUI

Requirements:

Note: In Linux you must to install the following packages: libcurl4-openssl-dev libssl-dev libxml2-dev

 sudo apt-get install libcurl4-openssl-dev libssl-dev libxml2-dev

Warning:

If you are using version 3.4.2 of R software environment, please update to the most recent version 3.4.3, because many of the R packages needed by JBiclustGE presents errors during their installation, due to incompatibilities with version 3.4.2.

To install or update R to release 3.4.3 in linux, you can run this shell script: Download

Windows and Linux Jar Installer

This installer works in both Operating Systems. Download

Instructions:

  1. Install Java SE Runtime Environment.
  2. Install R environment.
  3. Run installer.

For Windows:

    Press over "jbiclustge-installer", follow the instructions given by the installer.

For Linux: 

   First option: press the right button of the mouse over "jbiclustge-installer.jar", and choose "Open with Oracle Java 8 Runtime", follow the instructions given by the installer.

   Second option: open the  linux console, input the following commands,
       a) cd "path to folder where jbiclustge-installer.jar its stored", example "cd /home/user/"
       b) java -jar jbiclustge-installer.jar
       c) follow the instructions given by the installer

Linux Deb installer

Download

Install with package manager, or through linux console:

1. cd "path to folder where jbiclustge.deb its stored", example "cd /home/user/"
2. sudo dpkg -i jbiclustge.deb

Note: This process needs "SuperUser" privileges because the installation will be performed in opt/ directory.

JBiclustGE-CLI

Requirements:

Windows and Linux Jar Installer

This installer works in both Operating Systems. Download

Instructions:

  1. Install Java SE Runtime Environment.
  2. Run installer.

For Windows:

    1) Press over "jbiclustge-cli-installer.jar", follow the instructions given by the installer.
    2) Open the folder where you have installed the JBiclustGE-CLI, example:  C:\Users\"windows user"\JBiclustGE-CLI
    3) Press over "add_jbiclustge-cli_as_environment_variable" that is inside "JBiclustGE-CLI" folder.
    4) Open a Windows command line prompt "cmd".
    5) write command "jbiclustge-cli -h" to see instructions.
    6) write command "jbiclustge-cli -conf" to configure the JBiclustGE-CLI execution environment.

For Linux: 

   First option: press the right button of the mouse over "jbiclustge-cli-installer.jar", and choose "Open with Oracle Java 8 Runtime", follow the instructions given by the installer.

   Second option: open the  linux console, input the following commands,
       a) cd "path to folder where jbiclustge-cli-installer.jar its stored", example "cd /home/user/"
       b) java -jar jbiclustge-cli-installer.jar
       c) follow the instructions given by the installer

   Configure jbiclustge-cli as environment variable:
       a) Open the folder where you have installed the jbiclustge-cli.jar, by default installs in /home/"your_linux_username"/JBiclustGE-CLI
       b) Open the linux console, write commands:

              1) cd /home/"your_linux_username"/JBiclustGE-CLI
              2) sh add_jbiclustge-cli_as_environment_variable.sh

       c) close the current linux console, and open a new one.
       d) write the following commands:

              1) jbiclustge-cli -h  'this will allow you to check all the input commands'
              2) jbiclustge-cli -conf choosefolder  'this will do the initial configuration of JBiclustGE-CLI, and all the necessary R packages will be installed in the directory that you have chosen'

Linux Deb installer

Download

Install with package manager, or through linux console:

  1. cd "path to folder where jbiclustge-cli.deb its stored", example "cd /home/user/"
  2. sudo dpkg -i jbiclustge-cli.deb

Note: This process needs "SuperUser" privileges because the installation will be performed in opt/ directory. 

  Configure jbiclustge-cli:
      a) Open the linux console, write commands:

          1) jbiclustge-cli -h  'this will allow you to check all the input commands'
          2) jbiclustge-cli -conf choosefolder  'this will do the initial configuration of JBiclustGE-CLI, and all the necessary R packages will be installed in the directory that you have chosen'

Source Code

JBiclustGE API

The source code of JBiclustGE API it's in the following GitHub repository: link

Maven dependency:

 <dependency>
        <groupId>pt.uminho.ceb.biosystems</groupId>
        <artifactId>JBiclustGE</artifactId>
        <version>1.0.0-SNAPSHOT</version>
 </dependency>

add the following repository to your pom:

 <repository>
        <id>git-ornrocha</id>
        <url>https://github.com/ornrocha/thirdparty/raw/master/mvn-repo</url>
        <snapshots>
            <enabled>true</enabled>
            <updatePolicy>always</updatePolicy>
        </snapshots>
 </repository>

JBiclustGE-CLI and JBiclustGE-GUI

The executables concerning to JBiclustGE-GUI and JBiclustGE-CLI can be compiled directly from source code, the instructions are described in links presented below.

The source code of JBiclustGE-CLI it's in the following GitHub repository: link

The source code of JBiclustGE-GUI it's in the following GitHub repository: link