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fixed a typo

Author: kkmattil

docs/data/sensitive-data/images/desktop/sd-installer2.png

@@ -335,11 +335,15 @@ Each virtual Desktop (or virtual computer) is pre-built and contains a limited s
       * R + RStudio Server versions matched with Puhti r-env-singularity module (R 4.0.5 + RStudio Server 1.4.1106, MRAN, Bioconductor 3.12) 
       * [Rstudio 4.2.2 and all CRAN and Bioconductor libraries can be added with SD-software-installer](./r-in-sd-desktop.md)
 
+### SD Software installer
+
+[SD Software installer](./tutorials/sd-software-installer.md) provides easy-to-use tool to add some commonly used software to SD Desktop.
+
 ### Software customisation
 
-Users can install their user-level software to SD Desktop, but this requires technical expertise. As SD Desktop is isolated from the internet, you can't directly use installation tools like _git_, _coda_, _cpan_ or _pip_ as they are dependent on internet connections to external repositories. Further, SD Desktop users can't do any operation that needs superuser access.
+Users can install their own software to SD Desktop, but this requires technical expertise. As SD Desktop is isolated from the internet, you can't directly use installation tools like _git_, _coda_, _cpan_ or _pip_ as they are dependent on internet connections to external repositories. Further, SD Desktop users can't do any operation that needs superuser access.
 
-The most convenient way to add new software to your SD Desktop is to build a Singularity container outside SD Desktop and then import the Singularity image through SD Connect to SD Desktop. The two documents below describe two sample cases on adding software with containers.
+If you want to add new software to your virtual machine independently, the most convenient way to add new software to your SD Desktop is to build a Singularity container outside SD Desktop and then import the Singularity image through SD Connect to SD Desktop. The two documents below describe two sample cases on adding software with containers.
 
    1. [Importing ready-made software containers from a public repository to SD Desktop](./sd-desktop-singularity.md)
    2. [Creating you own Singularity container and importing it to SD Desktop](./creating_containers.md)

docs/data/sensitive-data/sd_desktop.md

@@ -0,0 +1,32 @@
+# Auto-apptainer
+
+Auto-apptainer is a help tool that can be used to add software to a SD Desktop virtual machine. It utilizes a library of
+of Apptainer based software contaners, pre-loaded by CSC. You can suggest a container to be added to the library.
+
+Auto apptainer is not available by default, but you must install it first using [SD Software installer](./sd-software-installer.md).
+After that you can lauch the tool with command:
+
+```test
+auto-apptainer
+```
+By deafault, this lists all the Apptainer packages available. From the list you can select the backage to be installed.
+
+Alternatively you can add a fltering criteria to the command. In this case only those containers whose name or one 
+of commands that the container provides, matches the search creiteria, are listed.
+
+For example command :
+
+```test
+auto-apptainer bam
+```
+
+asks the user to choose from two contaiers: _bamtools_ and _bedtools_. Bedtools is included as it provides commands _bamToBed_ and _bamToFasta_ that match the serach criteria in this case.
+
+Once a container is selected, one more apptainer warpper based commands are created to drectory: _/shared-directory/sd-tools/bin_.
+These commands can mostly be used like natively installed commands. For example after installing the Bamtools container, 
+Bamtools can be startted with command:
+
+```text
+bamtools
+```
+

docs/data/sensitive-data/tutorials/auto-apptainer.md

@@ -0,0 +1,87 @@
+# Adding Rstudio and R libraries to SD Desktop #
+
+Using R and Rstudio in SD Desktop virtual machines is based on a singularity container that 
+contains R and Rsudio installations and over 1000 commonly used R libraries. However, as there 
+are nearly 20 000 libraries in the CRAN repository and over 2000 libraries in the Bioconductor 
+repository, it is quite common that some library that you would like to use, is not included in the default selection. 
+
+This document describes the usage of help tools that you can use to add Rstudio 4.2.2 and missing R libraries to your SD Desktop environment. 
+The process described here is the first prototype implementation of this service and it is likely the change in the future.
+
+## Requirements ##
+
+In order to get access to the installation tool, you need to **send a request to servicedesk@csc.fi**.
+In the request, indicate that you wish that the SD Desktop software installation help tools would be made available for your project. 
+You must also include to the message the  **Project identifier string** of your project.
+
+You can check this random string for example in the [SD Connect service](https://sd-conenct.csc.fi). There you find the 
+Project Identifier in the **User information** view. 
+
+
+## Installing Rstudio 4.2.2 ##
+
+Log in to your SD Desktop and open **Data Gateway**. If the software installation help tools are enabled for your project, then you should have folder: 
+**tools-for-sd-desktop** included in the directory that Data Gateway created ( in Projects/SD Coonnect/_your-project-name_).
+Open _tools-for-sd-desktop_ folder and from there, drag/copy file **sd-installer.desktop** to your desktop.
+
+[![Installing-sd-installer](../images/desktop/sd-installer1.png)](../images/desktop/sd-installer1.png)
+
+**Figure 1.** Copying sd-installer.desktop file to SD desktop.
+ 
+Double click the copy of _sd-installer.desktop_ to start the software installation tool. Use this tool to install _Rstudio 4.2.2_ 
+to your SD Desktop virtual machine if you have not yet done so. The installation takes several minutes. 
+
+[![sd-installer](../images/desktop/sd-installer2.png)](../images/desktop/sd-installer2.png)
+
+**Figure 2.** SD software installation tool.
+
+Once the installation is done you can start Rstudio by clicking the Rstudio icon in the desktop or by executing command:
+
+```text
+start-rstudio
+```
+
+## Adding missing R libraries ##
+
+Once the Rstudio environment is installed, new libraries can be added by opening a terminal and executing command:
+```text
+add-R-library 
+```
+
+The command asks for a search term and shows the available R libraries that match the search string. 
+If several libraries are found, you will be provided an enumerated list from which you can
+select the library that should be installed.
+
+This tool does not check for internal library dependencies, and quite often the first installation attempt fails. 
+In these cases you should check the names of the missing libraries and install them first.
+
+For example, search term _fusion_ finds 8 libraries. In this case we want to install _DNAfusion_  (DNAfusion_1.0.0.tar.gz), 
+that is listed as the first in the list so the installation started by pressing _1_ and then  _Enter_.
+
+In this case, the installation however fails as DNAfusion depends on a library which is not yet installed. 
+In this kind of situations you need to check the names of the missing libraries from the error message and install them first. 
+You can give the name of the library as an argument to the add-R-library command. 
+For example in this case the missing library, _bamsignals_, can be added with command:
+```text
+add-R-library bamsignals
+```
+
+After which you can install DNAfusion
+
+```text
+add-R-library DNAfusion
+```
+
+The additional libraries are installed to location ”/shared-directory/sd-toold/apps/R/lib” where they are available for
+all the users of the virtual machine. This is not a default location of R libraries so you must define the location in your 
+R code with command:
+
+```text
+.libPaths(”/shared-directory/sd-tools/apps/R/lib/”)
+```
+
+After that you can take the library in use. e.g.
+
+```text
+library(DNAfusion)
+```

docs/data/sensitive-data/tutorials/rstudio.md

@@ -0,0 +1,90 @@
+# SD Desktop Software Installer
+
+As SD desktop virtual machines are isolated from internet, installing additional software and libraries 
+to your virtual machine is not straight forward. Adding extra software is possible, but it requires that 
+you convert the installation processes into files that can be uploaded to SD Connect and from there 
+copied to your SD Desktop environment for installation and usage.
+
+In generally, we recommend using Apptainer containers for importing the software you need.
+
+To make additional software installations easier, CSC has created **SD Software Installer** tool,
+that provides an easy way to add few commonly used software packages and help tools to your virtual machine. 
+This document describes the usage of this help tool.
+
+
+## Requirements ##
+
+In order to get access to the installation tool, you need to **send a request to servicedesk@csc.fi**.
+In the request, indicate that you wish that the SD software installer would be 
+made available for your project. You must include the  **Project identifier string** of your project to the request.
+You can check this 32 characters long random string for example in the [SD Connect service](https://sd-conenct.csc.fi). 
+There you find the Project Identifier in the **User information** view. 
+
+## Installing the SD Software Installer ##
+
+Log in to your SD Desktop and open **Data Gateway**. If the software installation help tools are enabled for your project,
+then you should have folder **tools-for-sd-desktop** included in the directory that Data Gateway created 
+( in Projects/SD-Connect/_your-project-name_).
+
+Open _tools-for-sd-desktop_ folder and from there, drag/copy file **sd-installer.desktop** to your desktop.
+
+[![Installing-sd-installer](../images/desktop/sd-installer1.png)](../images/desktop/sd-installer1.png)
+
+**Figure 1.** Copying sd-installer.desktop file to SD desktop.
+ 
+Double click the copy of _sd-installer.desktop_ to start the software installation tool. In Ubuntu based VMs you
+need to right-click the and select _Allow Launching_ before  you can use the _sd-installer.desktop_.
+
+[![sd-installer](../images/desktop/sd-installer2.png)](../images/desktop/sd-installer2.png)
+
+**Figure 2.** SD Software installer
+
+
+## Usage ##
+
+In order to use the installer, you must have an active Data Gateway connection running and 
+mounting of the SD Conncect data should be done through the default location in the file system 
+(_Projects_ directory in the users home directory). 
+
+The installer shows a panel of buttons that allow you to install a software by just cliking the button.
+The available software include graphical and command line applications. For graphical applications, a launching icon is added 
+to the desktop. All software is installed to directory _/shared-directory/sd-tools/_ where the installaion is availale for all the
+users of the virtual machine.
+
+In case of some applications, part of the installation process occurs only when the application is started for the first time.
+Thus you should start the application once after the installation, to make sure that the prcess is completed. After that
+the installaled software should work also when Data Gateway connection has not been opened.
+
+
+## Tool selection ##
+
+Notes about the available tools. Note that this list may be out-dated:
+
+### Statistics
+*  [Rstudio 4.2.2](rstudio.md) R statistics tool with graphcal user interface and help tools for adding libraries.
+*  [PSPP](https://www.gnu.org/software/pspp/) Open Source alternative for SPSS statistics tool.
+
+### Imaging and vidos
+*  [Audacity](https://www.audacityteam.org/). Sound editor.
+*  [OpenShot 3.1.1](https://www.openshot.org/). Video editor.
+   *  This tool works only in Ubuntu22 based VMs.
+   *  After installation, right click the OpenShot desktop icon and select: _Run as a program_.
+*  [QuPath 0.4.2](https://github.com/qupath/qupath/). Software for bioimage analysis.GATL
+*  [Whisper](whisper.md) Automatic speech recognition.
+  
+### Geosciences
+*  [QGis 3.1.1](https://qgis.org/en/site/) A Free and Open Source Geographic Information System. 
+   *   [QGis at CSC servers](../../../apps/qgis.md)
+
+### Biosciences
+*  [GATK](https://gatk.broadinstitute.org/hc/en-us) A genomic analysis toolkit focused on variant discovery.
+*  [MultiQC 1.10](https://multiqc.info/) NGS Read quolity checking tool.
+*  [Salmon 1.9.0](https://combine-lab.github.io/salmon/) Program to produce transcript-level quantification estimates from RNA-seq data
+   *   [Salmon 1.9.0 at CSC servers](../../../apps/salmon.md)
+
+### Miscallenius
+*   [auto-apptainer](./auto-apptainer.md) Tool to add command line applications using the Apptainer container library provided by CSC.
+*   [VS Code 1.78.2](./vscode.md) Code editor.
+*   [Crypt4gh-gui](../sd_connect.md#sensitive-data-encryption-and-upload-for-analysis-up-to-100-gb) Encryption tool.
+*   [Backup tool](./backup_sd_desktop.md) Help tool to automiatize backup and export in SD Desktop.
+

docs/data/sensitive-data/tutorials/sd-software-installer.md

@@ -0,0 +1,24 @@
+# VS Code
+
+VS Code is a code editor redefined and optimized for building and debugging modern web and cloud applications.
+
+VS Code 1.78.2 can be installed to a SD Desktop virtual machine with [SD software installer](./sd-software-installer.md).
+The installation creates a desktop button for VS Code
+
+The VS Code installation does not include any extensions. However you can add them yourself.
+
+On you own computer open VS Cone extension library:
+
+*   [https://marketplace.visualstudio.com/VSCode](https://marketplace.visualstudio.com/VSCode)
+
+Once you have found the right extension, use the _Download Extension_ function to
+download the extension to your local computer as a _.vsix_ file.
+
+Then use [SD Connect](https://sd-connect.csc.fi) to encrypt and upload the .vsix file to SD Connect.
+
+Then in SD Desktop, refresh the DataGateway connection and copy the _.vsix_ file to your
+SD Desktop environment.
+
+Finally open VS Code. Open the _extensions manager_ ( lowest icon, in the first column if the interface).
+In the Extensions manager, point the three dots ... to open the menu that contains function _Install from VSIX_
+Use that function to read in the .vsix file you imported.

docs/data/sensitive-data/tutorials/vscode.md

@@ -0,0 +1,18 @@
+# Whisper
+
+Whisper is a general-purpose speech recognition model. It is trained on a large dataset of 
+diverse audio and is also a multitasking model that can perform multilingual speech recognition, 
+speech translation, and language identification.
+
+*   [Whisper home page](https://github.com/openai/whisper)
+
+The installation in SD Desktop is based on [WhisperDO](https://github.com/nicholasgcotton/WhisperDO)
+
+After installation Whisper is available as a command line tool in SD Desktop. 
+Sample command:
+
+```text
+   whisper audio.mp3 --model medium
+```
+
+