In addition to the pre-installed software tools and built-in apps that come with your workspace, you can self-install other tools for analysis in your workspace VM. 

To facilitate your work, we've preloaded a variety of installers for popular tools, plus instructions for install, on your virtual desktop. For those that do not have instructions loaded in the t-drive, we've created written/video tutorials for you to follow (see graph below). *Note you will need to install the tools that are not already included in the data science virtual machine (DVSM) template before use. 

Approved External Software Tools

See a full list of additional tools approved by ADDI for workspace use, along with their installation instructions, below. 

Approved Tools	Preinstalled in DVSM - Windows	Preinstalled in DVSM - Linux	Instructions in t-drive?	Installation Instructions	Video installation tutorial	If nowhere, how to install?
Anaconda Python				Here	-	-
Annovar				Here	Video	-
Apache Spark 3.1 (standalone)				-	-	-
AzCopy				-	-	-
Azure CLI				-	-	-
Azure Cosmos DB Data Migration Tool				-	-	-
Azure SDK				-	-	-
Azure Storage Explorer				-	-	-
BCFtools				Here	Video	-
Bedtools				Here	Video	-
Bioconductor + DESeq2				Here	Video	-
Blob FUSE driver				-	-	-
BWA-MEM				-	-	Redistributable, standalone installer, added the BWA installer to the t-drive. Installing BWA comes with BWA-MEM included as it (BWA-MEM) is an algorithm of BWA. Installation instructions are very simple here: https://github.com/lh3/bwa#availability. Only dependency required is zlib, likely already installed in the VM. If not, use: sudo apt-get install zlib1g-dev and then proceed with BWA installation.
CatBoost				-	-	-
CellSNP				Here	Video	-
CRAN-R				-	-	-
Cromwell				Here	Video	-
CUDA, cuDNN, NVIDIA Driver				-	-	-
Database GUIs				Here	-	-
Dlib				-	-	-
Docker				Here	-	-
edgeR	-	-	-	-	-	This is an R package. User can simply install this package directly into an R session in the command terminal as long as R is installed. Specific installation instructions can be found here: https://bioconductor.org/packages/release/bioc/html/edgeR.html
Emacs				-	-	-
FreeSurfer				Here	Video	-
GATK				Here	Video	-
GCTA				Here	Video	-
Git (and Git Bash)				Here	-	-
GitLab				Here	-	-
H2O				-	-	-
Horovod				-	-	-
IBM SPSS Statistics				Here	Video	-
Intel MKL				-	-	-
IntelliJ IDEA				-	-	-
Julia (Julialang)				-	-	-
Jupyter Notebook Server				Here	-	-
JupyterHub				-	-	-
JupyterLab				-	-	-
Kallisto				-	-	Redistributable, standalone installer, added to t-drive for Linux and Windows
LibreOffice				Here	-	-
LightGBM				-	-	-
MAGeCK				Here	Video	-
Matlab				-	-	Users to directly download the MatLab installer from within the VM, the matlab site (https://www.mathworks.com/) has been whitelisted hub-wide.
MFlow R API				Here	-	-
Microsoft Edge Browser				-	-	-
MRIcron				Here	Video	-
Nano				-	-	-
Nccl				-	-	-
Node.js				-	-	-
Notepad++				-	-	-
NVidia-smi				-	-	-
ONNX Runtime				-	-	-
OpenCV				-	-	-
OpenJDK				-	-	-
PLINK				Here	Video	-
PLINK 1.9				Here	Video	-
PLINK 2.0				Here	Video	-
PostgreSQL				-	-	-
Power BI Desktop				-	-	-
PyCharm				Here	-	-
Python SDK				-	-	-
PyTorch				-	-	-
R				Here	-	-
Rattle				-	-	-
RStudio				Here	-	-
Salmon				-	-	Redistributable, standalone installer, added to t-drive for Linux (Windows installer doesn't exist). It can also be installed without the installer in the command terminal using conda, instructions here: https://combine-lab.github.io/salmon/getting_started/
Samtools				Here	Video	-
SAS				Here	-	-
Scanpy				Here	Video	-
Sleuth	-	-	-	-	-	This is an R package. User can simply install this package directly into an R session in the command terminal as long as R is installed. Prior to installation, user must first install the R packages "rhdf5" and "devtools" in this order, and then install "sleuth". Specific installation instructions can be found here: https://pachterlab.github.io/sleuth/download.html
STAR				-	-	Redistributable, standalone installer, added to t-drive for Linux (Windows installer doesn't exist). Compiling/installation instructions here: https://github.com/alexdobin/STAR/blob/master/README.md
Sublime Text				Here	-	-
SUPPA2	-	-	-	-	-	Not a standalone installer, can simply be installed using python in a command terminal. Requires python 3. Simply open up a terminal and type: "pip install SUPPA==2.3", or can use conda, as such: "conda install -c bioconda suppa". Instructions here: https://github.com/comprna/SUPPA
TensorFlow				-	-	-
TXimport	-	-	-	-	-	This is an R package. User can simply install this package directly into an R session in the command terminal as long as R is installed. Is possible that the BiocManager package may need to be installed first. This can also be installed in the R session, no standalone installer necessary.
Unix/Linux command-line tools				-	-	-
Upgrading Python				Here	Video	-
VCFTools				-	-	A package that can be installed directly in the command terminal using "sudo apt-get install vcftools"
Vim				-	-	-
VireoSNP				Here	-	-
Vowpal Wabbit				-	-	-
Weka				-	-	-
XGBoost				-	-	-
.NET Framework				-	-	-

Accessing installers from the t-drive 

Linux Virtual Desktop

1. Open the File System icon found on the desktop.  

2. Open the t_drive folder. This contains tools, their installers, and instructions for install. 

Windows Virtual Desktop

1. Open the Microsoft Azure Storage Explorer application from the Windows icon on the bottom left of the screen.

2. From the left folder navigation panel, select Storage Accounts > Attached Containers > Blob Containers > tdrive. 

3. The right panel will open with all tools, their installers, and instructions. 

Don't see your favorite tool?

Email support@alzheimersdata.org to request a security review and installation approval.