updates doc

README.md

@@ -2,23 +2,61 @@
 
 🦆🦆 Don't duck that QC thingy 🦆🦆
 
+## Who am I?
+
+QuaC is a pipeline developed using snakemake, which runs a set of selected QC tools on NGS samples.
+
 ## What can I quac about?
 
-* Somalier
-  * Relatedness
-  * Sex
-  * Ancestry
-* indexcov
-  * (Estimated) coverage of smaples
+| Tool                                                              | Use                                                        |
+| ----------------------------------------------------------------- | ---------------------------------------------------------- |
+| [somalier](https://github.com/brentp/somalier)                    | Estimation of sex, ancestry and relatedness                |
+| [verifybamid](https://github.com/Griffan/VerifyBamID)             | Estimates within-species (i.e. cross-sample) contamination |
+| [mosdepth](https://github.com/brentp/mosdepth)                    | Fast BAM/CRAM depth calculation                            |
+| [indexcov](https://github.com/brentp/goleft/tree/master/indexcov) | Estimate coverage from whole-genome bam or cram index      |
+| [covviz](https://github.com/brwnj/covviz)                         | Identifies large, coverage-based anomalies                 |
+
+
+## Installation
+
+Installation simply requires fetching the source code. Following are required:
+
+- Git
+- CGDS GitLab access
+- [SSH Key for access](https://docs.uabgrid.uab.edu/wiki/Cheaha_GettingStarted#Logging_in_to_Cheaha) to Cheaha cluster
+
+To fetch source code, change in to directory of your choice and run:
+
+```sh
+git clone -b master \
+    --recurse-submodules \
+    git@gitlab.rc.uab.edu:center-for-computational-genomics-and-data-science/sciops/pipelines/quac.git
+```
+
+Note that this repository uses git submodules, which gets automatically pulled when cloning using above command. Simply
+downloading this repository from GitLab, instead of cloning, may not fetch the submodules included.
+
+## Environment Setup
+
+### Requirements
 
+- Anaconda/miniconda
 
-## How to quac?
+Also the tools listed below, which are not available via conda distribution, need to be installed. Static binaries are
+available for both these tools and they are hence easy to install.
 
-* Modify config file `configs/workflow.yaml` as needed. Note: `projects_path` and `project_name` may be the most
-  important ones you would care about.
-* Pedigree file specific to the project is required. Should be stored as `data/raw/ped/<project_name>.ped`.
-* See the header of `workflow/Snakefile` for usage instructions on how to run the workflow
+- [somalier](https://github.com/brentp/somalier)
+- [goleft](https://github.com/brentp/goleft)
 
+*Note:* CGDS folks using QuaC in cheaha may skip this step, as these tools are already installed and centrally available.
+
+### Setup config file
+
+Workflow config file `configs/workflow.yaml` provides path to certain tool installation path as well as other files that
+the tools require. Modify them as necessary. Refer to the QC tool's documentation for more information on files that
+they require.
+
+### Create conda environment
 
 ```sh
 module reset
@@ -26,12 +64,22 @@ module load Anaconda3/2020.02
 
 # create conda environment. Needed only the first time.
 conda env create --file configs/env/quac.yaml
+# activate conda environment
+conda activate quac
 
-# if you need to update existing environment
+# if you need to update the existing environment
 conda env update --file configs/env/quac.yaml
 
-# activate conda environment
-conda activate quac
+```
+
+
+
+If the default path to `datasets_central` is going to be used (i.e. you'll be using the tool for testing and/or
+development), then you'll also need to initialize the default `datasets_central` directory. This can be done by running
+the following (must be done for each user):
+
+```sh
+mkdir -p $USER_SCRATCH/tmp/datasets_central_manager/datasets $USER_SCRATCH/tmp/datasets_central_manager/logs
 ```