README

1 files changed, 11 insertions, 75 deletions

diff --git a/README.md b/README.md
index 5d6f3fa..b5dc7f0 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,10 @@ This repository is used to rewrite and modernize the original GEMMA tool. The id
 
 GEMMA is the original software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. You can find the original code on [github](https://github.com/genetics-statistics/GEMMA). It may even build from this repo for the time being.
 
+NOTE: December 2024 main software development has moved to [PanGEMMA](https://git.genenetwork.org/pangemma/about/)!
+Pangemma is essentially a fork of GEMMA that is meant to scale up for pangenomics. We are also taking the opportunity to revamp the code base. GEMMA itself is in maintenance mode.
+
+
 Check out [RELEASE-NOTES.md](./RELEASE-NOTES.md) to see what's new in each release.
 
 * [Key features](#key-features)
@@ -42,62 +46,8 @@ WIP
 
 ## Run GEMMA
 
-GEMMA is run from the command line. To run gemma
-
-```sh
-gemma -h
-```
-
-a typical example would be
-
-```sh
-# compute Kinship matrix
-gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt \
-    -gk -o mouse_hs1940
-# run univariate LMM
-gemma -g ./example/mouse_hs1940.geno.txt.gz \
-    -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt \
-    -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8_lmm
-```
-
-Above example files are in the git repo and can be downloaded from
-[github](https://github.com/genetics-statistics/GEMMA/tree/master/example).
-
 ### Debugging and optimization
 
-GEMMA has a wide range of debugging options which can be viewed with
-
-```
- DEBUG OPTIONS
-
- -check                   enable checks (slower)
- -no-fpe-check            disable hardware floating point checking
- -strict                  strict mode will stop when there is a problem
- -silence                 silent terminal display
- -debug                   debug output
- -debug-data              debug data output
- -debug-dump              -debug-data, but store the data to files (grep write() calls for messages/names)
- -nind       [num]        read up to num individuals
- -issue      [num]        enable tests relevant to issue tracker
- -legacy                  run gemma in legacy mode
-```
-
-typically when running gemma you should use -debug which includes
-relevant checks. When compiled for debugging the debug version of
-GEMMA gives more information.
-
-For performance you may want to use the -no-check option. Also check
-the build optimization notes in [INSTALL.md](INSTALL.md).
-
-## Help
-
-+ [The GEMMA manual](doc/manual.pdf).
-
-+ [Detailed example with HS mouse data](example/demo.txt).
-
-+ [Tutorial on GEMMA for genome-wide association
-analysis](https://github.com/rcc-uchicago/genetic-data-analysis-2).
-
 ## Citing PanGEMMA
 
 PanGEMMA is not published yet.
@@ -132,35 +82,21 @@ studies.](https://doi.org/10.1101/042846) *Annals of Applied Statistics*, in pre
 
 ## License
 
-PanGEMMA Copyright (C) 2012–2025, Pjotr Prins, Xiang Zhou and others (see the soure file headers and git log).
-
-The *PanGEMMA* and *GEMMA* source code repository is free software: you can redistribute it under the terms of the [GNU General Public License](http://www.gnu.org/licenses/gpl.html). All the files in this project are part of *GEMMA*. This project is distributed in the hope that it will be useful, but **without any warranty**; without even the implied warranty of **merchantability or fitness for a particular purpose**. See file [LICENSE](LICENSE) for the full text of the license.
-
-Both the source code for the [gzstream zlib wrapper](http://www.cs.unc.edu/Research/compgeom/gzstream/) and [shUnit2](https://github.com/genenetwork/shunit2) unit testing framework included in GEMMA are distributed under the [GNU Lesser General Public License](contrib/shunit2-2.0.3/doc/LGPL-2.1), either version 2.1 of the License, or (at your option) any later revision.
+Copyright (C) 2012–2025, Pjotr Prins & Xiang Zhou
 
-The source code for the included [Catch](http://catch-lib.net) unit testing framework is distributed under the [Boost Software Licence version 1](https://github.com/philsquared/Catch/blob/master/LICENSE.txt).
+The *PanGEMMA* source code is free software: you can redistribute it under the terms of the [GNU General Public License](http://www.gnu.org/licenses/gpl.html). All the files in this project are part of *PanGEMMA*. This project is distributed in the hope that it will be useful, but **without any warranty**; without even the implied warranty of **merchantability or fitness for a particular purpose**. See file [LICENSE](LICENSE) for the full text of the license.
 
-## Optimizing performance
+The original source code for *GEMMA* that is part of *PanGEMMA* is distributed under the same GPL license.
 
-Precompiled binaries and libraries may not be optimal for your particular hardware. See [INSTALL.md](INSTALL.md) for speeding up tips.
-
-## Building from source
-
-More information on source code, dependencies and installation can be found in [INSTALL.md](INSTALL.md).
-
-## Input data formats
-
-## Contributing code, reporting a PanGEMMA bug or issue
-
-WIP
+The source code for the [gzstream zlib wrapper](http://www.cs.unc.edu/Research/compgeom/gzstream/) (still) included in GEMMA are distributed under the [GNU Lesser General Public License](contrib/shunit2-2.0.3/doc/LGPL-2.1), either version 2.1 of the License, or (at your option) any later revision.
 
 ## Code of conduct
 
-By using GEMMA and communicating with its communtity you implicitely agree to abide by the [code of conduct](https://software-carpentry.org/conduct/) as published by the Software Carpentry initiative.
+Being part of the PanGEMMA community and communicating with its communtity you implicitely agree to abide by the [code of conduct](https://software-carpentry.org/conduct/) as published by the Software Carpentry initiative.
 
 ## Credits
 
-The *PanGEMMA* software was developmed
+The *PanGEMMA* software was developed by
 
 [Pjotr Prins](http://thebird.nl/)<br>
 Dept. of Genetics, Genomics and Informatics<br>
@@ -172,5 +108,5 @@ The *GEMMA* software was developed by:
 Dept. of Biostatistics<br>
 University of Michigan<br>
 
-with contributions from Peter Carbonetto, Tim Flutre, Matthew Stephens,
+with (early) contributions from Peter Carbonetto, Tim Flutre, Matthew Stephens,
 and [others](https://github.com/genetics-statistics/GEMMA/graphs/contributors).