From 0f638714f41a0145e637c4fbbef90b73feb3b9b0 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Mon, 3 Jul 2023 15:56:57 +0100
Subject: [PATCH] update README

---
 README.md | 86 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 84 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 651cc1b..220e09f 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,85 @@
-# hattivatti
+# `hattivatti`
 
-> A Finnish [job submitter](https://github.com/ebi-gdp/jobsubmitter).
+`hattivatti` submits [`pgsc_calc`](https://github.com/PGScatalog/pgsc_calc) jobs
+to [Puhti HPC](https://docs.csc.fi/computing/systems-puhti/) at CSC. Jobs are
+configured to execute in a secure way because genomes are sensitive
+data. `hattivatti` is a proof of concept for testing sensitive data submission
+to CSC.
+
+## Run `hattivatti`
+
+See [Releases](https://github.com/ebi-gdp/hattivatti/releases) for most recent
+stable versions of `hattivatti`. The development version can be run with:
+
+```
+$ git clone https://github.com/ebi-gdp/hattivatti.git --branch dev
+$ cargo run
+```
+
+## Documentation
+
+```
+$ cargo doc --open
+```
+
+## Deployment notes
+
+Puhti is currently on RHEL 7 with an old version of glibc.
+
+Github actions builds with rust-buster to match glibc version (2.28).
+
+### Cronjob
+
+cron shell doesn't load much:
+
+```
+$ # load 'module' command
+$ source /appl/profile/zz-csc-env.sh
+```
+
+### Set environment variables
+
+Sensitive variables:
+
+```
+$ export GLOBUS_SECRET_TOKEN=<...>
+$ export AWS_ACCESS_KEY_ID=<...>
+$ export AWS_SECRET_ACCESS_KEY=<...>
+$ export NXF_SINGULARITY_CACHEDIR=<...>
+```
+
+Configuration variables:
+
+```
+$ export RUST_LOG=info
+$ export NXF_SINGULARITY_CACHEDIR=<path>
+```
+
+### Clone pgsc_calc
+
+```
+$ cd /scratch/projec_XXXXXX/
+$ nextflow clone https://github.com/PGScatalog/pgsc_calc.git
+```
+
+### Run hattivatti
+
+```
+$ hattivatti --schema-dir repo/data/schemas  --work-dir work
+```
+
+### Backup database (optional)
+
+After hattivatti executes the database will have no connections.
+
+```
+$ module load allas
+$ rclone copy work/hattivatti.db s3allas://bucket/hattivatti/hattivatti.db
+```
+
+### Software dependencies
+
+* `curl`
+* `jq`
+* `nextflow`
+  * `java 16`
-- 
GitLab