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.

Approved External Software Tools

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

Approved Tools	Preinstalled in DSVM - Windows	Preinstalled in DSVM - Linux	Installation Instructions	Video installation tutorial	If nowhere, how to install?
Anaconda Python	✅	✅	Here	-	-
Annovar				Video	-
Apache Spark 3.1 (standalone)	✅	✅	-	-	-
AzCopy	✅		-	-	-
Azure CLI	✅	✅	-	-	-
Azure Cosmos DB Data Migration Tool	✅		-	-	-
Azure SDK	✅	✅	-	-	-
Azure Storage Explorer	✅	✅	-	-	-
BCFtools			Here	Video	-
Bedtools				Video	-
Bioconductor + DESeq2				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				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				Video	-
GATK				Video	-
GCTA				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				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				Video	-
Nano	✅		-	-	-
Nccl		✅	-	-	-
Node.js	✅	✅	-	-	-
Notepad++	✅		-	-	-
NVidia-smi	✅	✅	-	-	-
ONNX Runtime		✅	-	-	-
OpenCV		✅	-	-	-
OpenJDK	✅	✅	-	-	-
PLINK			Here	Video	-
PLINK 1.9				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				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				Video	-
VCFTools			-	-	A package that can be installed directly in the command terminal using "sudo apt-get install vcftools"
Vim		✅	-	-	-
VireoSNP				-	-
Vowpal Wabbit	✅	✅	-	-	-
Weka			-	-	-
XGBoost	✅	✅	-	-	-
.NET Framework	✅		-	-	-

Tech Help

GNPC Harmonized Dataset