Installation

There are two ways to work with inventa:

A) Running inventa with Binder:

Binder allows to run inventa on the cloud with a Binder instance, which is really convenient but you need to save the parameters and results locally as these instances are shutting down after 15 min of inactivity.

(this may take several minutes to build Jupyter assets … please wait).

how to use Binder?

All the necessary tables described below can be ‘drag & drop’ in the folder data/ direclty in the browser, you’ll find the folder in the left side.
The output can be found in the folder results/ as a TAB separated file.
If needed, you can modify the jupyter notebook directly in the browser (make sure to save it locally).
As explained below, if needed, you can modify the inventa.py parameters inside src/inventa.py, this can be done as well directly in the browser.

B) Running inventa locally:

Install the conda environment

First make sure to have anaconda installed.

Clone the repo locally

First clone the repository using git clone in command line. You may need to install the git package (see here):

git clone https://github.com/luigiquiros/inventa.git

Create a new conda environment to avoid clashes:

conda env create -n inventa -f inventa/environment.yml

Then, activate the environment:

conda activate inventa

If you need to update the environment run: [make sure to run the following to keep the depencies versions]

conda env update --file environment.yml

and the submodules

git pull --recurse-submodules

If you have an error, try installing scikit-bio from conda-forge before create the environment:

conda install -c conda-forge scikit-bio

Also, is possible to have the following error: ‘Microsoft Visual C++ 14.0 or greater is required (install Microsoft C++ Build Toold from https://visualstudio.microsoft.com/visual-cpp-build-tools/)’. To solve it please make sure you include the installation of the workload Desktop development with C++

Inventa