feat: Update environment setup

Functional-Genomics-Lab · May 24, 2022 · 36e2f1d · 36e2f1d
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diff --git a/docs/00-overview.md b/docs/00-overview.md
@@ -7,19 +7,19 @@ sidebar_label: 'Overview'
 
 # Overview
 
-| WEEK | TUESDAY                                        | THURSDAY                                  |
-| ---: | ---------------------------------------------- | ----------------------------------------- |
-|    1 | Introduction/[Setup Environment](./week_01.md) | Intro to Unix                             |
-|    2 | [Reproducible Computing](./week_02/intro.md)   | Group Project 1 Introduction Lab          |
-|    3 | Transcriptomics                                | [Intro to nf-core](week_04/nf-core)       |
-|    4 | Tertiary Analysis Intro                        | Group Project Demo Day                    |
-|    5 | Epigenomics                                    | [Jupyter on Slurm](week_05/jupyter_slurm) |
-|    6 | Epigenomics                                    | [Jupyter on Slurm](week_05/jupyter_slurm) |
-|    7 | ChIP-seq                                       | ChIP-seq                                  |
-|    8 | Mutations                                      | Group Project 2 Demo Day                  |
-|    9 | Intro to module 3 project/Nextflow Scripting   | Nextflow Scripting                        |
-|   10 | Intro to Variant Calling                       | Variant Calling Continued/Xena Browser    |
-|   11 | Project Work Day                               | Group Demo Day/Concluding Remarks         |
+| WEEK | TUESDAY                                                          | THURSDAY                                  |
+| ---: | ---------------------------------------------------------------- | ----------------------------------------- |
+|    1 | Introduction/[Setup Environment](./week_01/environment_setup.md) | Intro to Unix                             |
+|    2 | [Reproducible Computing](./week_02/intro.md)                     | Group Project 1 Introduction Lab          |
+|    3 | Transcriptomics                                                  | [Intro to nf-core](week_04/nf-core)       |
+|    4 | Tertiary Analysis Intro                                          | Group Project Demo Day                    |
+|    5 | Epigenomics                                                      | [Jupyter on Slurm](week_05/jupyter_slurm) |
+|    6 | Epigenomics                                                      | [Jupyter on Slurm](week_05/jupyter_slurm) |
+|    7 | ChIP-seq                                                         | ChIP-seq                                  |
+|    8 | Mutations                                                        | Group Project 2 Demo Day                  |
+|    9 | Intro to module 3 project/Nextflow Scripting                     | Nextflow Scripting                        |
+|   10 | Intro to Variant Calling                                         | Variant Calling Continued/Xena Browser    |
+|   11 | Project Work Day                                                 | Group Demo Day/Concluding Remarks         |
 
 # Course Alumni
 

diff --git a/docs/week_01/_category_.json b/docs/week_01/_category_.json
@@ -0,0 +1,4 @@
+{
+  "label": "Week 1",
+  "position": 1
+}
diff --git a/docs/week_01.md → docs/week_01/environment_setup.md b/docs/week_01.md → docs/week_01/environment_setup.md
@@ -1,8 +1,8 @@
 ---
-id: week-1
+id: env
 title: Environment Setup
 description: ''
-sidebar_label: 'Week 1'
+sidebar_label: 'Environment Setup'
 sidebar_position: 1
 ---
 
@@ -110,18 +110,20 @@ MacOS:
 
 - [iTerm2](https://iterm2.com/downloads.html)
 
-## Intro to Unix
+## [Biostar Handbook: 8. Installing on a Computer Cluster](https://www.biostarhandbook.com/cluster-setup.html#cluster-setup)
 
-Practical Research Computing Unix Lecture [^1]
+We'll be following the text book for this section!
 
-### Some basic commands
+You'll need to run
 
-You don't need to make flashcards to memorize them. Luckily if you're at a
-command line, you probably have access to a search engine, and what they do or
-what they were is just a search away.
+```sh
+module load anaconda3
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
 
-We're going to run through [The Missing Semester: The
-Shell](https://missing.csail.mit.edu/2020/course-shell/) together.
+curl http://data.biostarhandbook.com/install/conda.txt | xargs conda install -q -y
+```
 
 # Assignment 1