diff --git a/jupyter-book/_static/default_text_env_setup.md b/jupyter-book/_static/default_text_env_setup.md index 6fe10cdf..15e41a80 100644 --- a/jupyter-book/_static/default_text_env_setup.md +++ b/jupyter-book/_static/default_text_env_setup.md @@ -1,8 +1,12 @@ -1. **Save the yml content**: +1. **Install conda**: + + - Before creating the environment, ensure that [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) is installed on your system. + +2. **Save the yml content**: - Copy the content from the yml tab into a file named `environment.yml`. -2. **Create the environment**: +3. **Create the environment**: - Open a terminal or command prompt. - Run the following command: @@ -10,7 +14,7 @@ conda env create -f environment.yml ``` -3. **Activate the environment**: +4. **Activate the environment**: - After the environment is created, activate it using: ```bash @@ -21,7 +25,7 @@ name: ``` -4. **Verify the installation**: +5. **Verify the installation**: - Check that the environment was created successfully by running: ```bash conda env list diff --git a/jupyter-book/conditions/gsea_pathway.ipynb b/jupyter-book/conditions/gsea_pathway.ipynb index a6f568c9..b0929817 100644 --- a/jupyter-book/conditions/gsea_pathway.ipynb +++ b/jupyter-book/conditions/gsea_pathway.ipynb @@ -4,25 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n", - ":class: dropdown\n", - "\n", - "`````{tab-set}\n", - " \n", - "````{tab-item} Steps\n", - "```{include} ../_static/default_text_env_setup.md\n", - "```\n", - "````\n", - "\n", - "````{tab-item} yml\n", - "```{literalinclude} gsea_pathway.yml\n", - ":language: yaml\n", - "```\n", - "````\n", - "\n", - "`````\n", - "\n", - "``````" + "{bdg-link-primary-line}`Env Setup <#this-is-a-test>`" ] }, { @@ -32,7 +14,7 @@ "source": [ "(enrichment-analysis)=\n", "\n", - "# Gene set enrichment and pathway analysis " + "# Gene set enrichment and pathway analysis" ] }, { @@ -2116,6 +2098,33 @@ "session_info.show()" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "(this-is-a-test)=\n", + "## Environment setup\n", + "\n", + "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n", + "\n", + "`````{tab-set}\n", + " \n", + "````{tab-item} Steps\n", + "```{include} ../_static/default_text_env_setup.md\n", + "```\n", + "````\n", + "\n", + "````{tab-item} yml\n", + "```{literalinclude} gsea_pathway.yml\n", + ":language: yaml\n", + "```\n", + "````\n", + "\n", + "`````\n", + "\n", + "``````" + ] + }, { "cell_type": "markdown", "metadata": {}, diff --git a/jupyter-book/conditions/perturbation_modeling.ipynb b/jupyter-book/conditions/perturbation_modeling.ipynb index ea4591ef..dde0695a 100644 --- a/jupyter-book/conditions/perturbation_modeling.ipynb +++ b/jupyter-book/conditions/perturbation_modeling.ipynb @@ -2,7 +2,15 @@ "cells": [ { "cell_type": "markdown", - "id": "cc96c027", + "id": "understanding-memory", + "metadata": {}, + "source": [ + "# Perturbation modeling" + ] + }, + { + "cell_type": "markdown", + "id": "d9e767e9", "metadata": {}, "source": [ "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n", @@ -26,14 +34,6 @@ "``````" ] }, - { - "cell_type": "markdown", - "id": "understanding-memory", - "metadata": {}, - "source": [ - "# Perturbation modeling" - ] - }, { "cell_type": "markdown", "id": "5e1ff7c8",