diff --git a/docs/00-overview.md b/docs/00-overview.md index 02d9331..5632430 100644 --- 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 new file mode 100644 index 0000000..b345218 --- /dev/null +++ b/docs/week_01/_category_.json @@ -0,0 +1,4 @@ +{ + "label": "Week 1", + "position": 1 +} \ No newline at end of file diff --git a/docs/week_01.md b/docs/week_01/environment_setup.md similarity index 88% rename from docs/week_01.md rename to docs/week_01/environment_setup.md index fa85118..1bdd2ff 100644 --- a/docs/week_01.md +++ b/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