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authorPjotr Prins2024-12-09 11:39:28 +0100
committerPjotr Prins2024-12-09 11:39:28 +0100
commitbae23cea43f8074757246f252dd22b4205b87199 (patch)
treeff90c1d9be842a595b47a82334c23e4ed09d0f5c /INSTALL.md
parent97d5d23552863b7ddcb1b629f16b9c7cd815c926 (diff)
downloadpangemma-bae23cea43f8074757246f252dd22b4205b87199.tar.gz
Update READMEs for new PanGEMMA development
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-# INSTALL GEMMA: Genome-wide Efficient Mixed Model Association
+# INSTALL PanGEMMA: Genome-wide Efficient Mixed Model Association
-## Check version
-
-Simply run gemma once installed
-
- gemma
-
-and it should give you the version.
-
-## GEMMA dependencies
-
-GEMMA runs on Linux, MAC OSX and Windows (with Docker). The runtime
-has the following dependencies:
-
-* C++ tool chain >= 5.5.0 (see Travis CI and we test with file .guix-dev-gcc-older)
-* GNU Science library (GSL) 2.x (GEMMA dropped support for GSL 1.x)
-* blas/openblas
-* lapack
-* zlib
-
-See below for installation on Guix.
-
-## Install GEMMA
-
-### Debian and Ubuntu
-
-Travis-CI uses Ubuntu for testing. Check the test logs for version numbers.
-
-[![Build Status](https://travis-ci.org/genetics-statistics/GEMMA.svg?branch=master)](https://travis-ci.org/genetics-statistics/GEMMA)
-
-Current settings can be found in [travis.yml](.travis.yml).
-
-### Bioconda
-
-(Note Bioconda install is a work in [progress](https://github.com/genetics-statistics/GEMMA/issues/52)
-
-Recent versions of GEMMA can be installed with
-[BioConda](http://ddocent.com/bioconda/) without root permissions using the following
-command
-
- conda install gemma
-
-### FreeBSD
-
-Recent editions of FreeBSD ports include [GEMMA](https://www.freebsd.org/cgi/ports.cgi?query=gemma&stype=all)
-
-### GNU Guix
-
-The GNU Guix package manager can install recent versions of [GEMMA](https://www.gnu.org/software/guix/packages/g.html)
-using the following command
-
- guix package -i gemma
-
-A more recent version may be found in the guix-bioinformatics channel
-which is maintained by the authors. See the
-[README](http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics), e.g.
-
- env GUIX_PACKAGE_PATH=./guix-bioinformatics guix package -A gemma
-
-To build GEMMA from source you can opt to install the build tools with
-GNU Guix, the current build container is in [guix.scm](guix.scm). See the first lines on how to create one using `guix shell`.
-
-An alternative is the command line invocation of [guix-dev](./.guix-dev)
-
- source .guix-dev
- make
-
-Guix allows for easy versioning. To build with an older gcc, for
-example:
-
- guix environment -C guix --ad-hoc gcc-toolchain@9.3.0 gdb gsl openblas zlib bash ld-wrapper perl vim which
-
-### Install with Docker
-
-Recent version of GEMMA come with a 64-bit Docker image that should run
-on Linux, Windows and MacOS.
-
-### Install from source
-
-Install listed dependencies (you may want to take hints from
-the Travis-CI [tests](./.travis.yml)) and run
-
- make -j 4
-
-(the -j switch builds on 4 cores).
-
- time make check
-
-You can run gemma in the debugger with, for example
-
- gdb --args \
- ./bin/gemma -g example/mouse_hs1940.geno.txt.gz \
- -p example/mouse_hs1940.pheno.txt -a example/mouse_hs1940.anno.txt \
- -snps example/snps.txt -nind 400 -loco 1 -gk -debug -o myoutput
-
-Note that if you get <optimized out> warnings on inspecting variables you
-should compile with GCC_FLAGS="" to disable optimizations (-O3). E.g.
-
- make WITH_OPENBLAS=1 GCC_FLAGS=
-
-Other options, such as compiling with warnings, are listed in the
-Makefile.
-
-### GNU Guix commands used
-
-Some development examples. With git bisect build the older versions
-of gemma with openblas
-
- ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl lapack openblas zlib bash ld-wrapper perl ldc
- make clean ; make WITH_OPENBLAS=1 FORCE_DYNAMIC=1 -j 8
-
-or with atlas
-
- ~/.config/guix/current/bin/guix environment -C guix --ad-hoc gcc gdb gfortran:lib gsl lapack atlas zlib bash ld-wrapper perl ldc
- make clean ; make WITH_OPENBLAS= FORCE_DYNAMIC=1 -j 25
-
-## Run tests
-
-GEMMA includes the shunit2 test framework (version 2.0).
-
- make check
-
-or
-
- ./run_tests.sh
-
-## Releases
-
-### Docker release
-
-To distribute GEMMA I made static versions of the binary. A container
-can be made instead with, for example
-
-```sh
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics ~/.config/guix/current/bin/guix \
- pack -f docker gemma-gn2 -S /bin=bin
-```
-
-which created a container in of size 51MB. Tiny! For more information
-see
-[GUIX-NOTES](http://git.genenetwork.org/guix-bioinformatics/guix-notes/CONTAINERS.org).
-
-
-### Static release
-
-To create a static release, locate the gfortran lib and use
-
- source .guix-dev-static
- make WITH_GFORTRAN=1 EXTRA_FLAGS=-L/gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib static
-
-otherwise OpenBlas will complain with
-
- undefined reference to `_gfortran_concat_string'
-
-Note you can use guix.scm if you load with
-
- guix shell -L ~/guix-pjotr -C -D -f guix.scm
+WIP