From 316b2e8b587457d8dfa7cfb583c0872a66a99377 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Thu, 29 Feb 2024 08:18:50 +0100
Subject: [PATCH] docs: adding repository overview section (#5)

---
 src/doc_repooverview.rst | 165 +++++++++++++++++++++++++++++++++++++++
 src/index.rst            |   1 +
 2 files changed, 166 insertions(+)
 create mode 100644 src/doc_repooverview.rst

diff --git a/src/doc_repooverview.rst b/src/doc_repooverview.rst
new file mode 100644
index 0000000..3ace7fe
--- /dev/null
+++ b/src/doc_repooverview.rst
@@ -0,0 +1,165 @@
+.. _doc_repooverview:
+
+===============
+GitHub Overview
+===============
+
+This section gives an overview of the GitHub repositories relevant to the VarFish project.
+All are in ``varfish-org``, version 2.0 of the Apache license is used.
+
+.. _doc_repooverview_direct_importance:
+
+-----------------
+Direct Importance
+-----------------
+
+The following repositories are directly important and provide functionality used by the system.
+
+.. list-table::
+    :header-rows: 1
+
+    * - name
+      - license
+      - synopsis
+    * - annonars
+      - MIT
+      - precomputed variant, region, and gene annotation
+    * - annonars-data-clinvar
+      - MIT
+      - ClinVar data builds for annonars
+    * - cada-prio
+      - MIT
+      - phenotype-based prioritization based on knowledge graph embeddings
+    * - cadd-rest-api
+      - MIT
+      - REST API wrapper for CADD-scripts
+    * - cadd-rest-api-mock
+      - MIT
+      - mocking the CADD REST API server for VarFish development
+    * - clinvar-data-jsonl
+      - MIT
+      - weekly ClinVar releases as JSONL plus useful aggregation
+    * - clinvar-this
+      - MIT
+      - ClinVar submission and XML dump file parsing
+    * - mehari
+      - MIT
+      - transcript effect annotation and tx model information
+    * - mehari-data-tx
+      - MIT
+      - transcript data builds for mehari
+    * - varfish-db-downloader
+      - MIT
+      - Snakemake workflow to download public data
+    * - varfish-cli
+      - MIT
+      - command line interface for VarFish REST API
+    * - varfish-dev-docs
+      - MIT
+      - documentation for developers
+    * - varfish-docker-compose-ng
+      - MIT
+      - setup VarFish with Docker Compose
+    * - varfish-server
+      - MIT
+      - VarFish web server
+    * - varfish-server-worker
+      - MIT
+      - heavy lifting in varfish-server written in Rust
+    * - viguno
+      - Apache
+      - HPO ontology access and full-text search
+
+
+.. _doc_repooverview_indirect_importance:
+
+-------------------
+Indirect Importance
+-------------------
+
+The following are dependencies of the one in :ref:`doc_repooverview_direct_importance` maintained by us and housekeeping tools.
+
+.. list-table::
+    :widths: 30 20 50
+    :header-rows: 1
+
+    * - name
+      - license
+      - synopsis
+    * - biocommons-bioutils-rs
+      - Apache
+      - (partial) port of biocommons/bioutils to Rust
+    * - hgvs-rs
+      - Apache
+      - port of biocommons/hgvs to the Rust programming language
+    * - rocksdb-utils-lookup
+      - Apache
+      - utility library for using RocksDB as lookup tables
+    * - seqrepo-rs
+      - Apache
+      - a port of biocommons/seqrepo to the Rust programming language
+
+
+.. _doc_repooverview_experimental:
+
+------------
+Experimental
+------------
+
+The following contain experimental, under development, or unfinished code.
+
+.. list-table::
+    :header-rows: 1
+
+    * - name
+      - license
+      - synopsis
+    * - scarus
+      - Apache
+      - automated evaluation of ACMG rules
+    * - varfish-clinical-beacon-client
+      - MIT
+      - client for clinical beacons API proof of concept
+    * - varfish-wf-validation
+      - MIT
+      - Snakemake workflow for automated validation
+    * - varfish-cli-ng
+      - MIT
+      - VarFish CLI based on aws-smithy
+
+
+.. _doc_repooverview_legacy:
+
+------
+Legacy
+------
+
+The following are legacy repositories.
+
+.. list-table::
+    :header-rows: 1
+
+    * - name
+      - license
+      - synopsis
+    * - varfish-course-scripts
+      - MIT
+      - scripts for generating the data used in the VarFish course
+    * - varfish-wf-queries
+      - MIT
+      - VarFish (Snakemake) Client Workflow for Querying Snakemake
+    * - varfish-docker-compose
+      - MIT
+      - legacy setup VarFish as using Docker Compose
+    * - varfish-anno
+      - MIT
+      - convert annotation database files to Var:fish: import format
+    * - varfish-installer
+      - MIT
+      - use varfish-docker-compose instead
+    * - varfish-annotator
+      - MIT
+      - annotate variants for import into VarFish server
+    * - varfish-data-igsr
+      - MIT
+      - repository for building IGSR data sets for use in VarFish
diff --git a/src/index.rst b/src/index.rst
index 5547d3a..9fae0c2 100644
--- a/src/index.rst
+++ b/src/index.rst
@@ -10,3 +10,4 @@ VarFish Development Docs
     doc_architecture
     doc_dataflows
     doc_futureplans
+    doc_repooverview