blob: eb75a09705fb9b5612238e538a0f8da2e991a495 (
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
|
# 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 and MAC OSX and the runtime has the following
dependencies:
* C++ tool chain
* GNU Science library (GSL) 1.x (does not currently work with GSL >= 2).
* blas
* [Eigen library](http://eigen.tuxfamily.org/dox/)
* zlib
See below for installation on Guix.
## Install GEMMA
### 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
### 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
To install the build tools with GNU Guix
guix package -i make gcc linux-libre-headers gsl eigen openblas lapack glibc ld-wrapper
### Install from source
Install listed dependencies and run
make -j 4
(the -j switch builds on 4 cores).
if you get an Eigen error you may need to override the include
path. E.g. on GNU Guix with shared libs and DEBUG the following may
work
make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1 WITH_OPENBLAS=1 DEBUG=1
to run GEMMA tests
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
Other options, such as compiling with warnings, are listed in the
Makefile.
## Run tests
GEMMA includes the shunit2 test framework (version 2.0).
make check
or
./run_tests.sh
|
