Command-line

After configuring the JbiclustGE-CLI as explained in the setup section, users can perform four diferent operations:

Establishment of a "profile", that is a configuration to execute the biclustering algorithms with a given gene expression dataset. This profile can be created in both JBiclustGE-GUI and JBiclustGE-CLI.
Execution of the biclustering methods based on a "profile" configuration.
Establishment of a configuration to perform the Gene Set Enrichment Analysis (GSEA), of the results produced in the execution of a "profile".
Execution of GSEA based on the previous configuration.

Setting up a Biclustering "Profile"

Open the Windows/Linux console
Write input command:
```
jbiclustge-cli -newprofile
```
Several questions will be asked to the user, in order to build the configuration. Important steps:
There is a step that is asked if gene expression has missing values, make sure if your dataset has missing values or not, because if the dataset has missing values and you define as not having missing values, that can lead to errors when you try to execute the algoritms in a later stage.
When is asked which methods that you want to execute, you can choose "all", and delete the configuration file corresponding to the methods that you do not want to execute, in the "algorithms" folder.
After creating your biclustering "profile" you have to configure the settings of each one the biclustering methods that are present in the "algorithms" folder, inside the folder that is shown in the final of the creation process of the "profile".
If you choose to execute the Gene Set Enrichment Analysis (GSEA) in runtime, you have also to configure the settings present in "Ontologizer_configuration.conf" or "topGO_configuration.conf" files (it will depend of the GSEA engine that you have chosen).
The gene expression dataset will be copied for the "profile" folder that you have defined, and be named as "dataset".

A "profile" can be loaded in two ways:

a) Directly, using the following command:

jbiclustge-cli -run /path_to_your_profile/

b) Using a command to open a help graphical dialog for selecting the folder of a "profile".

jbiclustge-cli -run choosefolder

Open the Windows/Linux console
Write input command:
```
jbiclustge-cli -newgsea
```
Several questions will be asked to the user, in order to build the configuration.
When is asked: "Please set the path of the folder of executed profile", choose the folder where the results of biclustering algorithms were saved, by default is a folder named as "Results_biclustering".
When is asked: "Please set the file path of the gene expression dataset, used in the biclustering analysis", choose the gene expression datatset that was used in biclustering analysis, by default is the file "dataset" present in the "profile" folder.
Configure the settings present in "Ontologizer_configuration.conf" or "topGO_configuration.conf" files (it will depend of the GSEA engine that you have chosen).

Write input command in console:

jbiclustge-cli -rungsea /path_to_gsea_configuration (Ontologizer_configuration.conf or topGO_configuration.conf)

The results will be saved within the corresponding folder of the biclustering results or in the folder defined by the user (if user have chosen in the previous configurations, to save in a custom folder).