STATOOLS - OVERVIEW

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1.1 - ABOUT STATOOLS

STATools is the Client-Desktop App provided by the GPRO suite to manage a collection of scripts developed in R and other programming languages for statistical analysis and graphical representation of biological data and results (including Tests, ANOVA, Plots, Histograms, Heatmaps, Venn diagrams, Cluster and Diversity analysis, KRONAs, Networks and more). Scripts 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 a interface-based solution to easily manage the scripts. The App provides a menu to access the interfaces and a left side space to visualize the results.

1.2 - VERSION

The current version of STATools 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 STATOOLS IN YOUR PC

STATools is Java standalone software that can be 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 “STATools.exe” and execute/run it.

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

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

1.4 - GETTING FAMILIAR

The layout of STATools is based on the following features; “Directory Browser”, “Working Space”, “Results Preview” and “Menu”.

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

             WORKING SPACE FOR INTERFACES: Central working space to launch the interfaces of all R scripts.

             MENU: To choose the script and analysis.

1.5 - SERVER SIDE DEPENDENCIES

STATools is a Client Side + Server Side solution thus meaning that the application is coupled via API with a bioinformatic infrastructure called GPRO Server Side that contains all the dependencies needed by VariantSeq to execute the workflows and pipelines. These dependencies are scripts, databases and the following third party CLI software:

• System requirements:
  • Linux Operating System with minimum Bash version 4.
  • Apache HTTP server 2.2 or later.
  • PHP 5.
  • R (Recommended version 3.4)
  • Other scripts created by Biotechvana to handle clients connections and run jobs/pipelines.
• R libraries:
  • Gplots Gregory W. et al. 2016. gplots.
  • RColorBrewer Neuwirth E. 2014. RColorBrewer.
  • GMD Zhao X. et al. 2016. GMD.
  • devtools Wickham H. et al. 2018. devtools.
  • htmlwidgets Vaidyanathan R. et al. 2018. htmlwidgets.
  • heatmaply Galili T. et al. 2018. heatmaply.
  • pheatmap Kolde R. 2018. pheatmap.
  • cluster Maechler M. et al. 2018. cluster.
  • multtest Katherine SP. et al. 2005. multtest.
  • Hmisc Harrell Jr F. et al. 2018. Hmisc.
  • fpc Hennig C. 2018. fpc.
  • ggbiplot Q. Vu V. 2015. ggbiplot.
  • WVPlots Mount J. et al. 2018. WVPlots.
  • agricolae Mendiburu F. 2017. agricolae.
  • genefilter Gentleman R. et al. 2018. genefilter.
  • siggenes Schwender H. 2012. siggenes.
  • affy Gautier L. et al. 2004. affy.
  • gcrma Wu J. et al. 2018. gcrma.
  • biomaRt Durinck S. et al. 2009. biomaRt
  • EMA Servant N. et al. 2016. EMA.
  • vegan Oksanen J. et al. 2018. vegan.
  • Marbl/krona Ondov B. et al. 2016. Marbl/krona.
  • ape Paradis E. et al. 2018. ape.
  • ade4 Dray S. et al. 2018. ade4.
  • doParallel Calaway R. et al. 2017. doParallel.
  • foreach Calaway R. et al. 2017. foreach.
  • ggplot2 Wickham H. 2016. ggplot2
  • picante Kembel S. et al. 2018. picante.
  • plyr Wickham H. 2016. plyr.
  • RJSONIO Temple Lang D. 2014. RJSONIO.
  • scales Wickham H. 2017. scales.
  • testthat Wickham H. et al. 2017. testthat.
  • GUniFrac Chen J. 2018. GUniFrac.
  • ggtree Yu G. et al. 2017. ggtree.

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 STATOOLS WITH THE SERVER SIDE

Once the GPRO server side docker has been installed you need to link VarianSeq 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. User name 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 VariantSeq (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

1.7 - RAM ASSIGNATION TO YOUR PC

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

Within the “STATools.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 STATools, 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.

GPRO licensing and Usage           Former versions           TSI-100903-2019-11

Biotechvana

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