DENOVOSEQ - OVERVIEW


1.1 - ABOUT DENOVOSEQ

DeNovoSeq is the Client-Desktop App provided by the GPRO suite to manage and run pipelines for de novo assembly and annotation (publication in preparation). Pipelines and all other backend dependencies can be installed in the user PC if it has RAM enough or more properly in a remote server. The software is coupled with the server infrastructure providing the user with an interface-based solution to easily manage pipelines and databases. In particular, DeNovoSeq provides an FTP system to upload/download archives from your computer to the server or vice versa, a tracking system. In similar way to other solutions like Galaxy Project (Afgan et al 2018), DeNovoSeq provides a collection of interfaces where the different steps of the de novo assembly and annotation workflow (quality analysis, preprocessing, de novo assembly, gene prediction, annotation, and functional characterization) are organized by an intuitive menu that considers different protocols to perform the analysis.

1.2 - VERSION

The current version of DeNovoSeq is 2.0, which is distributed within the GPRO suite 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 DENOVOSEQ IN YOUR PC

DeNovoSeq is a Java application that can be easily installed on PCs with at least 2GB of RAM and that have installed the Java Runtime Environment (Java JDK) version 11 or above.

To check if you already have a JDK installed, open a command line interface and type:

java -version
If you have the java version 11.0_xx, you should see the following message:
$ java -version
jopenjdk 11.0.14.1 2022-02-08
OpenJDK Runtime Environment (build 11.0.14.1+1-Ubuntu-0ubuntu1.20.04)
OpenJDK 64-Bit Server VM (build 11.0.14.1+1-Ubuntu-0ubuntu1.20.04, mixed mode, sharing)
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 archive utility program e.g WinRAR. Then browse to the executable file “DeNovoSeq.exe” and execute/run it.

To install the Mac version:
Extract the archive to the desired destination using:
$ unzip DeNovoSeq.x.y.os.zip
Then browse to the executable binary file “DeNovoSeq.app” and execute/run it.

To install the Linux version:
Extract the archive to the desired destination using:
$ unzip DeNovoSeq.x.y.os.zip
Then browse to the executable binary file “DeNovoSeq” and execute/run it.
NOTE: Take into account that the view of the following manual can change depending on the Operative System used.

1.4 - GETTING FAMILIAR

The layout of DeNovoSeq is based on the following Features: “Directory Browser”, “FTP Browser”, "Working Space” and the Top Menu.

Figure 1: Basic layout of DeNovoSeq. The Directory Browser and Working space can be resized clicking on the icons at the right top. DeNovoSeq also provides mouse-based functions to manage files and folders at the directory browser and/or the FTP.


DIRECTORY BROWSER: to set any folder of your PC as directory for storing the files managed by DeNovoSeq.

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

WORKING SPACE FOR PIPELINE INTERFACES: central working space for DeNovoSeq to open the pipeline interfaces.

TOP MENU: the main menu of the tool to manage the data, choose the pipelines to select/use execution mode a track processes running in the server.
DIRECTORY: PREPROCESSING: DE NOVO ASSEMBLY AND POST-ASSEMBLY: GENE PREDICTION FUNCTIONAL GENE ANNOTATION: PREFERENCES: HELP:

1.5 - SERVER SIDE DEPENDENCIES

The pipelines managed by DeNovoSeq need the following dependencies be installed in your server:

The GPRO Server Side can be installed in the PC of the user or in remote servers as a Cloud Computing resource. However, its installation is a complex task due to the lot of dependencies and requirements (besides of the CLI software) for installing and running this infrastructure. For this reason, we distribute the GPRO Server Side in a Docker container that can be easily installed for the user in a couple of steps. Indications for installation of the GPRO Server Side Docker are available here.


1.6 - LINKING DENOVOSEQ WITH THE SERVER SITE

Once the GPRO server side docker has been installed you need to link DeNovoSeq to it. To do this, go to [Preferences → Pipeline connection settings] in the top menu and type the following into the configuration Dialog (Fig.2):

  1. Your email address: to receive notifications from the server.
  2. Host address: here you should type localhost (see figure 2) .
  3. Port number: This field should be filled inly in case of you run the server side manually. The default number will be 22.
  4. Username and password Your ID credentials provided to access the host server

As also shown in Figure 2 you can also check the option “Run GPRO server locally using Docker” to let you to automatically start the GPRO container each time you run DeNovoSeq (Also note that if you have this option checked you do not need to type the port). You can test if the app is connected to the Server Side clicking on the tab “Test connection settings”. Alternatively, if you install the Server Side manually (without the Docker) just add the IP of the remote server where the Server Side is hosted, add the port information (by default 22) and keep the Option “Run GPRO server locally using Docker” unchecked.

Figure 2: Server connection dialog.


In case you would need to connect the server infrastructure via Proxy, DeNovoSeq will require to be configured. You can choose one of the three following methods:
  1. If you do not know the proxy settings, choose the "Use system proxy settings" option to let DeNovoSeq to guess the default proxy settings already configured in your computer.
  2. If you know your proxy settings, you can 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.
  3. If you have a Proxy Automatic Configuration file (.pac) URL, use it for loading settings automatically from a remote file.
Figure 3: Proxy configuration (only if your server uses proxy).


1.7 - RAM ASSIGNATION IN YOUR PC

The RAM assigned to DeNovoSeq can be modified editing two parameters (Xms and Xmx) in the configuration file named “DeNovoSeq.ini”. In Linux and Windows computers, the “DeNovoSeq.ini” configuration file is located inside DeNovoSeq app folder. On macOS computers, this configuration file can be found by right-clicking on DeNovoSeq.app → Show package contents → Contents → MacOS → DeNovoSeq.ini.

Within the “DeNovoSeq.ini” file, Xms and Xmx parameters look like this:

- Xms1024m (Minimum allocated memory)
- Xmx2048m (Maximum allocated memory)

The values correspond to the assigned RAM in Megabytes. To modify the RAM assigned to DeNovoSeq, just change these values. Please keep in mind that the limitation depends on the amount of RAM of your computer. E.g. if your computer has 8GB of RAM, it is recommended to assign Xms2048m and Xmx4096m for a better performance. Xmx can be even increased up to Xmx6144m.but please avoid to use RAM values near to the maximum available memory of your PC as this election might provoke unstability in computer’s operating system.

1.8 - BASICS ABOUT THE DENOVOSEQ INTERFACE

A typical DeNovoSeq interface present at least two sections: one for managing the input and output files and folders and another one for options configuration and parameters (as shown in Figure 4). The procedure is always the same; from the FTP browser select the input file/s with the mouse and drag it/them to their respective fields. You can do the same with the folders you do want to use for depositing the output. Then, fill any other mandatory fields at the input/output field. Once the job input fields and the parameters have been fulfilled and/or configured you only need to click to start button at the end the interface form to run the Job, if the job has been successfully launched you will get a confirmation message. Otherwise, revise again all input and outputs upload and the options if any.

Figure 4: Example of “Input/Output” interface panel to uploading input files and output folders.








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