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
- Open the File System icon found on the desktop.
- Open the t_drive folder. This contains tools, their installers, and instructions for install.
Windows Virtual Desktop
- Open the Microsoft Azure Storage Explorer application from the Windows icon on the bottom left of the screen.
- From the left folder navigation panel, select Storage Accounts > Attached Containers > Blob Containers > tdrive.
- 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.