Installing Additional Software
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 | ✅ | ✅ | - | - | |
Annovar | Video | - | |||
Apache Spark 3.1 (standalone) | ✅ | ✅ | - | - | - |
AzCopy | ✅ | - | - | - | |
Azure CLI | ✅ | ✅ | - | - | - |
Azure Cosmos DB Data Migration Tool | ✅ | - | - | - | |
Azure SDK | ✅ | ✅ | - | - | - |
Azure Storage Explorer | ✅ | ✅ | - | - | - |
BCFtools | - | ||||
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 | Video | - | |||
CUDA, cuDNN, NVIDIA Driver | ✅ | ✅ | - | - | - |
Database GUIs | - | - | |||
Dlib | ✅ | - | - | - | |
Docker | - | - | |||
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) | ✅ | ✅ | - | - | |
GitLab | - | - | |||
H2O | ✅ | - | - | - | |
Horovod | ✅ | - | - | - | |
IBM SPSS Statistics | - | ||||
Intel MKL | ✅ | - | - | - | |
IntelliJ IDEA | ✅ | - | - | - | |
Julia (Julialang) | ✅ | ✅ | - | - | - |
Jupyter Notebook Server | ✅ | ✅ | - | - | |
JupyterHub | ✅ | - | - | - | |
JupyterLab | ✅ | ✅ | - | - | - |
Kallisto | - | - | Redistributable, standalone installer, added to t-drive for Linux and Windows | ||
LibreOffice | - | - | |||
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 | - | - | |||
Microsoft Edge Browser | ✅ | ✅ | - | - | - |
MRIcron | Video | - | |||
Nano | ✅ | - | - | - | |
Nccl | ✅ | - | - | - | |
Node.js | ✅ | ✅ | - | - | - |
Notepad++ | ✅ | - | - | - | |
NVidia-smi | ✅ | ✅ | - | - | - |
ONNX Runtime | ✅ | - | - | - | |
OpenCV | ✅ | - | - | - | |
OpenJDK | ✅ | ✅ | - | - | - |
PLINK | - | ||||
PLINK 1.9 | Video | - | |||
PLINK 2.0 | - | ||||
PostgreSQL | ✅ | - | |||
Power BI Desktop | ✅ | - | |||
PyCharm | ✅ | ✅ | - | ||
Python SDK | ✅ | ✅ | - | ||
PyTorch | ✅ | ✅ | - | ||
R | - | ||||
Rattle | - | ||||
RStudio | - | - | |||
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 | - | ||||
SAS | - | ||||
Scanpy | - | ||||
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 | - | ||||
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 | ✅ | - | - | - |