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Rnaseq - Overview


1.1 - ABOUT RNASEQ

RNAseq is the GPRO software manager to select and run pipelines for differential expression and enrichment analyses via cloud computing in remote servers where all the programs required for the different stages of the RNAseq analysis (quality analysis, preprocessing, mapping, transcriptome assembly and/or quantification, differential expression, enrichment) have been previously installed.

The application provides a FTP system to upload/download archives from the computer to the server or vice versa, a tracking system, as well as an interface system based on two modes (pipeline and step-to-step). The pipeline mode where the user only need to prepare a configuration file select the pipeline and run all the steps in one run or in an step-to-step mode where the tool provides an interface for each step providing access for all the tools available for that step and their different options.

1.2 - VERSION

The current version of RNAseq application is 2.0, which is distributed as an installer for Windows 7 (64 bit), a self-extracting disk image for Mac OS X 10.6 or later (64 bit), and a compressed tarball archive for Linux 2.6 kernel series or later (64 bit).

1.3 - INSTALLING RNASEQ IN YOUR PC

Every software application of the GPRO suite are Java standalone that require at least tools that can be easily installed in personal computers (PCs) with 2GB of RAM or higher as well as installation of a Java JRE (Java Runtime Environment) version 6 or superior.

To check if you already have a JRE installed on your computer:
Open a command line interface.
Type: java -version
Then, you should see a message like the following:

$ java -version
java version "1.8.0_92"
Java(TM) SE Runtime Environment (build 1.8.0_92-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode)
If you get a “Command not found” error message, it means that JRE is not installed.
For installing JRE, go to the official JRE repository here and download the version matching your operating system. Once installed, check again the output of java -version command on a command line interface. Sometimes, although the JRE is installed, it is not set at the path.

To install the Windows version
Extract the archive using archiver utility program e.g WinRAR. Then browse to the executable file “RNAseq.exe” and execute/run it.

To install the Mac version
Extract the archive to the desired destination using:
- tar xvf RNASeq.x.y.os.zip
Then browse to the executable binary file “RNAseq.app” and execute/run it.

To install the Linux version
Extract the archive to the desired destination using:
- tar xvf RNASeq.x.y.os.zip
Then browse to the executable binary file “RNAseq” and execute/run it.

1.4 - GETTING FAMILIAR

The software layout of RNAseq is structured into three components [Directory Browser, FTP Browser and working space for pipeline interfaces] and two menus [top menu and the step-to-step pipeline interface menu].


THE DIRECTORY BROWSER let you to select any directory of your PC as directory to store the files you manage with RNAseq or that you transfer between your PC and the remote server or vice versa.

THE FTP BROWSER is the File Transfer Protocol (FTP) of RNAseq letting you to access your server account and transfer files and folders from the directory browser to the server or vice versa. You only need to drag the files or folders you want to transfer from one side to another.

WORKING SPACE FOR PIPELINE INTERFACES: This is the central working space of RNAseq where the pipeline interfaces of RNAseq are launched.

The directory and FTP Browsers and the Working space can be resized as convenience or masked clicking on the icons they provide to the right top corner.

TOP MENU is the main menu of the tool the below detailed functions to manage the data, choose the pipelines to use and the running mode, and/or track the steps of the analysis.

DIRECTORY: TRANSCRIPTS PROTOCOL: PIPELINE JOBS: PREFERENCES: HELP: STEP-TO-STEP PIPELINE INTERFACE MENU: This is the specific menu for managing the pipelines interfaces for step-to step- analyses. This menu varies depending on the protocol and it is described in more detail within the Section "Step-to-step mode usage".

MOUSE FUNCTIONS
RNAseq provides additional functions to manage files and folders either on the directory browser and/or the FTP browser positioning and right clicking the mouse therein.

1.5 - SERVER DEPENDENCIES

The pipelines managed by RNAseq need you to install the following in your server.

A tutorial for installation of all software depencies of RNAseq is available here.

1.6 - TESTING THE SERVER CONNECTION

After running RNAseq program, you have to setup configuration to connect to the remote server. From the main menu select “Preferences → Pipeline connection settings”. Enter in the pipeline Configuration Dialog the Following:

  1. Your email address : Default email address to receive notifications from the server
  2. Host address : The address of the server you want to connect to
  3. Port number : port number for using ssh. Default is 22
  4. User name and password : your user credentials that have been created for you in the host server
To test if you are connected with the server click on the button “Test connection settings”. If you are connected you will be noticed as indicated in the figure below.


Otherwise, if you need to connect the server via Proxy, RNAseq will require to be configured. You can choose one of the three following methods:

If you do not know the proxy settings, you can choose the "Use system proxy settings" for letting RNAseq to guess the default proxy settings already configured in your computer.

If you know your proxy settings, you can mannualy specify the proxy configuration. This is the preferred option when using a network proxy. User, password and FTP settings are optional. The port for HTTP proxy is usually 8080 by default.

If you have a Proxy Automatic Configuration file (.pac) URL, you can use it for loading settings automatically from a remote file.









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