From fa8c5df7e9aa383fce6481e8b23222be4694ad88 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 26 Sep 2024 11:17:35 -0400
Subject: [PATCH] docs: clean up docs site for next release

remove under construction sections
---
 docs/getting-started.md | 63 -----------------------------------------
 docs/index.md           |  6 ----
 docs/release-guide.md   | 41 ---------------------------
 mkdocs.yml              |  3 --
 4 files changed, 113 deletions(-)
 delete mode 100644 docs/getting-started.md
 delete mode 100644 docs/release-guide.md

diff --git a/docs/getting-started.md b/docs/getting-started.md
deleted file mode 100644
index 33ebd4c..0000000
--- a/docs/getting-started.md
+++ /dev/null
@@ -1,63 +0,0 @@
-# Getting Started with CRISPIN
-
-TODO intro paragraph
-
-## Installation
-
-CRISPIN is installed on the Biowulf and FRCE clusters as part of the
-`ccbrpipeliner` module.
-If you'd like to run the pipeline in a different execution environment,
-take a look at [how to run the nextflow pipeline directly](nextflow.md).
-
-## Prepare a sample sheet
-
-TODO
-
-## Initialize
-
-Copy the configuration files to your current working directory
-
-```sh
-crispin init
-```
-
-## Run
-
-TODO preview, stub, mode=slurm
-
-TODO required params
-
-Run preview to view processes that will run:
-
-```sh
-crispin run -profile test -preview
-```
-
-Launch a stub run to view processes that will run and download containers:
-
-```sh
-crispin run -profile test,singularity -stub
-```
-
-Run the test dataset using the test profile:
-
-```sh
-crispin run -profile test,singularity
-```
-
-or explicitly specify the output directory and input:
-
-```sh
-crispin run -profile singularity --outdir results/test --input assets/samplesheet_test.csv
-```
-
-### Custom reference genome
-
-TODO different required params
-
-Create and use a custom reference genome:
-
-```sh
-crispin run -profile test -entry MAKE_REFERENCE
-crispin run -profile test -c results/test/genome/custom_genome.config
-```
diff --git a/docs/index.md b/docs/index.md
index b4655ed..4ef7e8e 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -3,9 +3,3 @@
 --8<-- "README.md"
 
 <!--- write additional info that you only want to appear in the docs index here -->
-
-Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
-
-It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
-
-Also include a workflow image to summarize the pipeline.
diff --git a/docs/release-guide.md b/docs/release-guide.md
deleted file mode 100644
index 0372e91..0000000
--- a/docs/release-guide.md
+++ /dev/null
@@ -1,41 +0,0 @@
-# Release Guide
-
-## How to test a pre-release on biowulf
-
-Install the development version of crispin.
-
-```sh
-# activate the conda env for development
-. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
-conda activate py311
-
-# go to the source on biowulf and update
-cd /data/CCBR_Pipeliner/Pipelines/CRISPIN/crispin-dev
-git pull
-# optionally switch to different branch if needed
-
-# install the version to a hidden path (e.g. .v0.1.0, .v1.0.0.9000) in /data/CCBR_Pipeliner/Pipelines/CRISPIN
-cd ..
-pip install ./crispin-dev -t ./.v0.1.0
-# add it to your PATH and PYTHONPATH with:
-export PATH="$PATH:/data/CCBR_Pipeliner/Pipelines/CRISPIN/.v0.1.0/bin/"
-export PYTHONPATH="$PYTHONPATH:/data/CCBR_Pipeliner/Pipelines/CRISPIN/.v0.1.0/"
-```
-
-## Add CRISPIN to the ccbrpipeliner module on biowulf
-
-Create a lua file in `/data/CCBR_Pipeliner/modules/ccbrpipeliner`, e.g. `dev.lua`.
-You can copy the most recent lua file to use as a base, then modify the following line:
-
-```lua
-source_sh("bash", "/data/CCBR_Pipeliner/Pipelines/CRISPIN/crispin-dev/bin/install.sh .v0.1.0")
-```
-
-Change the version of CRISPIN as needed. Notice the dot (`.`) in front of the version number to indicate a hidden path.
-
-Then use and load the module (substitute `dev` for whatever you named the new lua file) with:
-
-```sh
-module use /data/CCBR_Pipeliner/modules
-module load ccbrpipeliner/dev
-```
diff --git a/mkdocs.yml b/mkdocs.yml
index ca52862..9e5ca5d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -90,9 +90,6 @@ markdown_extensions:
 # Page Tree
 nav:
   - Home: index.md
-  - Usage:
-      - Getting Started: getting-started.md
   - Developer Guide:
       - How to contribute: contributing.md
-      - Release guide: release-guide.md
   - Changelog: changelog.md