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21 changes: 20 additions & 1 deletion GoogleCloud/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -52,4 +52,23 @@ As seen in the image above, we will download sequence files from the Google buck
+ Submodule 4, **Beyond Basic BASH** begins with a reminder of all the BASH commands covered in earlier lessons and combine complex commands with a loop and BASH scripting to iterate over several files with a single command.
+ Submodule 5, **Software Management** uses the Conda package manager to create and install environments where software can be installed.
+ Submodule 6, **Putting It All Together** leverages all of the skills learned in earlier lessons to download data from the SRA, create a Conda environment for genome assembly and annotation, check the quality, assemble, and annotate a genome. Then create a Google bucket and write a finalized file set to the Google bucket.
+ Submodule 7, **Error Mitigation** provides strategies for mitigating common coding errors.
+ Submodule 7, **Error Mitigation** provides strategies for mitigating common coding errors.

### Gemini (Optional)

Generative AI is available for this tutorial in the form of Gemini if you would like to use it. To run it, please reference submodule05 or run the following code within a submodule notebook.

```!pip install -q google-generativeai google-cloud-secret-manager
!pip install -q git+https://github.com/NIGMS/NIGMS-Sandbox-Repository-Template.git#subdirectory=llm_integrations
!pip install -q ipywidgets

import sys
import os
util_path = os.path.join(os.getcwd(), 'util')
if util_path not in sys.path:
sys.path.append(util_path)

from gemini import run_gemini_widget, create_gemini_chat_widget
from IPython.display import display

run_gemini_widget()
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