Tool Library
The tool library is a set of ready to use apps and work flows that are maintained by DNAnexus There are different categories and you can search by name of the tool as well.
The in-product Tools Library contains a more limited selection of tools than that available on the DNAnexus Platform. Users may not add tools to restricted projects on the TRE, from outside the TRE. Below are all of the tools available by default and whether or not they are able to be used within restricted projects.
Name of App
App ID
Summary
Restricted?
Unrestricted?
AWS S3 Importer
app-GzfPg9j0J04VkJQ99Xy1gx4P
Imports files from an external S3 bucket
No
Yes
Cloud Workstation
app-Gx3K7pQ5xX1j2BPvbbYbFqVX
Linux-based command line sandbox
No
Yes
Dataset Extender
app-GyXVXqj95z2QGzJ0QJ1vg61J
Extends an existing Dataset with new, derived data
No
Yes
JupyterLab with Python, R, Stata, ML, Image Processing
app-Gyb1zV80G4bVb50Qbk4v73XZ
Initiates a JupyterLab server that allows for analyses to be interactively performed in a Jupyter notebook run on the DNAnexus platform
Yes
Yes
JupyterLab with Spark Cluster
app-Gzb9F400PG9XgJ37JFVf699Y
Initiates a fully-managed, on-demand Spark cluster on the DNAnexus platform for big data processing and translational informatics
Yes
Yes
PLINK GWAS
app-Gz9YP180pzxjk45Y6k65b70z
Performs genome-wide association analysis at a large scale
Yes
Yes
Rebase Cohorts and Dashboards
app-GyXVXvj9Fz0B1ykFp7g6yfZz
Rebases cohorts and or dashboards onto the provided target dataset
Yes
Yes
REGENIE
app-GyXVXvj9Fz0B1ykFp7g6yfZz
Genome-wide association analysis of large cohorts for quantitative and binary phenotypes
Yes
Yes
REGENIE Marker Association Tests (Step 2)
app-Gy97Jg80G0zxXv6g2jF7p536
Tests a large set of markers for association
Yes
Yes
REGENIE Whole Genome Regression (Step 1)
app-Gy97GZj09QY873zb93k53v1Z
Fits a whole genome regression model to a subset of genetic markers
Yes
Yes
Swiss Army Knife
app-Gzz43k89X6KBv4q1yyb5zPQ0
Multi-purpose analysis tool
Yes
Yes
Table Exporter
app-GyXVY1j93Z2fv1g7ZJ3G42Qv
Exports a Spark SQL database to a CSV file
No
Yes
Tarball App Builder (Focal)
app-GvF9QQ00X24VZP0KX48gy5b8
Builds an app from a tarball for Ubuntu Focal
No
Yes
Tarball App Builder (Noble)
app-Gvkb3bj0370p6v958XF4bbP8
Builds an app from a tarball for Ubuntu Noble
No
Yes
Tarball App Builder (Xenial v1)
app-GvFq3P80643PZFp405G69J29
Builds an app from a tarball for Ubuntu Xenial
No
Yes
Tarball Applet Builder (Focal)
app-GvF9g180q3Pb73qp6X1xPPk6
Builds an applet from a tarball for Ubuntu Focal
No
Yes
Tarball Applet Builder (Noble)
app-GvkZqF00P9bP540kF1Y2P31F
Builds an applet from a tarball for Ubuntu Noble
No
Yes
Tarball Applet Builder (Xenial v1)
app-GvFpxQ8004FZjyQbKBPxQ11Q
Builds an applet from a tarball for Ubuntu Xenial
No
Yes
URL Fetcher
app-GyFjZyj53923gQZXGfyQFXYX
Fetches (uploads) a file from a provided URL
No
Yes
Steps to finding Tool Documentation
Navigate to the Tool Library (highlighted in gold)
In the “Any Name” search box, start entering “Swiss....”
Click on the tool name (in this example Swiss Army Knife)
This will direct you to the info tab of the tool .If you want the same version that is loaded automatically, this is all that you will need to do.
If you want a different version, navigate to the version dropdown and select the one you are wanting.
You can also select “Run” to run the app directly from the tool library, or you can run the app from the project space
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