Example Notebook: Finding data for your research organism: Plants and RNA-Seq

Delivered as a webinar for NCBI on August 18, 2021

Adelaide Rhodes, Ph.D,

Access this Binder by clicking the blue badge above or at the following URL:

https://mybinder.org/v2/gh/ncbi/finding-data-demo-08-21/HEAD

Interactive Notebook Environment

This is a Binder-compatible repo to support the demo notebook for an NCBI Minute Webinar Delivered on August 18, 2021. The notebook will continue to work after the webinar.

If you want to use this notebook on your own machine, be sure to install the requirements found in the binder folder.

Here us an explanation of the files in the binder folder.

• environment.yml - conda installs for relevant python packages

• apt.txt - tools loaded using apt on an ubuntu server (e.g. for samtools, type sudo apt install samtools -y

• postBuild - postbuild installation script - these programs can be loaded on your notebook server by running this as a bash script. To load these programs on a local machine, just change the script to replace /srv/conda/bin to usr/local/bin or another location in $PATH to use the commands as written in the notebook.

More Binder Notes

The environment.yml file should list all Python libraries on which your notebooks depend, specified as though they were created using the following conda commands:

conda activate example-environment
conda env export --from-history -f environment.yml

Note that the only libraries available to you will be the ones specified in the environment.yml, so be sure to include everything that you need!

Also note that if you skip the --from-history, conda may include OS-specific packages in environment.yml, which you would have to manually prune from environment.yml. For example, confirmed macOS-specific packages that should be removed are:

• libcxxabi=4.0.1
• appnope=0.1.0
• libgfortran=3.0.1
• libcxx=4.0.1