blob: f5c02b9b0b7ee4ff55f67edf9a7592a417df8e7c (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
|
# INSTALL GEMMA: 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.
[](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'
|
