forked from poldrack/fmri-analysis-vm
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Vagrantfile
181 lines (151 loc) · 5.67 KB
/
Vagrantfile
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
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
# this was adapted from nipype Vagrantfile
VAGRANTFILE_API_VERSION = "2"
$script = <<SCRIPT
if [ ! -d $HOME/miniconda ]
then
# install anaconda
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
chmod +x miniconda.sh
./miniconda.sh -b
rm -rf miniconda.sh
echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .env
fi
wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 0xA5D32F012649A5A9
echo 'deb http://cran.cnr.Berkeley.edu/bin/linux/ubuntu trusty/' > /tmp/cran.sources.list
sudo cp /tmp/cran.sources.list /etc/apt/sources.list.d/
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo rm -rf /var/lib/apt/lists /var/cache/apt/archives
sudo apt-get update -y
#sudo DEBIAN_FRONTEND=noninteractive apt-get -y -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold" dist-upgrade -y
# workaround http://forums.debian.net/viewtopic.php?f=10&t=101659
sudo /usr/share/debconf/fix_db.pl
sudo apt-get install -y dictionaries-common
sudo /usr/share/debconf/fix_db.pl
sudo apt-get install -y r-base \
git \
fsl-core \
fsl-atlases \
lxde \
lightdm \
chromium-browser \
wget \
tar \
unzip
# install nipype dependencies
$HOME/miniconda/bin/conda update --yes conda
$HOME/miniconda/bin/conda install --yes pip \
numpy \
scipy \
nose \
traits \
networkx \
dateutil \
ipython-notebook \
matplotlib \
statsmodels \
boto \
pandas \
scikit-learn \
spyder \
sympy
$HOME/miniconda/bin/pip install nibabel nilearn nipy
$HOME/miniconda/bin/pip install --upgrade https://github.com/nipy/nipype/archive/master.zip
$HOME/miniconda/bin/pip install --process-dependency-links git+https://github.com/pymc-devs/pymc3
if [ ! -d $HOME/mcr ]
then
echo "destinationFolder=$HOME/mcr" > mcr_options.txt
echo "agreeToLicense=yes" >> mcr_options.txt
echo "outputFile=/tmp/matlabinstall_log" >> mcr_options.txt
echo "mode=silent" >> mcr_options.txt
mkdir -p matlab_installer
wget -nc --quiet http://www.mathworks.com/supportfiles/downloads/R2015a/deployment_files/R2015a/installers/glnxa64/MCR_R2015a_glnxa64_installer.zip -O $HOME/matlab_installer/installer.zip
unzip $HOME/matlab_installer/installer.zip -d $HOME/matlab_installer/
./matlab_installer/install -inputFile mcr_options.txt
echo "export LD_LIBRARY_PATH=$HOME/mcr/v85/runtime/glnxa64:$HOME/mcr/v85/bin/glnxa64:$HOME/mcr/v85/sys/os/glnxa64:\\$LD_LIBRARY_PATH" >> .bashrc
echo "export LD_LIBRARY_PATH=$HOME/mcr/v85/runtime/glnxa64:$HOME/mcr/v85/bin/glnxa64:$HOME/mcr/v85/sys/os/glnxa64:\\$LD_LIBRARY_PATH" >> .env
echo "export PATH=$HOME/mcr/v85/bin/:\\$PATH" >> .bashrc
echo "export PATH=$HOME/mcr/v85/bin/:\\$PATH" >> .env
rm -rf matlab_installer mcr_options.txt
fi
if [ ! -d $HOME/spm12 ]
then
wget --quiet http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_r6472_Linux_R2015a.zip -O spm12.zip
unzip spm12.zip
echo 'alias spm="$HOME/spm12/run_spm12.sh $HOME/mcr/v85/"' >> .bashrc
echo 'alias spm="$HOME/spm12/run_spm12.sh $HOME/mcr/v85/"' >> .env
rm -rf spm12.zip
fi
if [ ! -d $HOME/ANTs.2.1.0.Debian-Ubuntu_X64 ]
then
echo "downloading ANTs"
wget --quiet https://github.com/stnava/ANTs/releases/download/v2.1.0/Linux_Ubuntu14.04.tar.bz2
tar jxvf Linux_Ubuntu14.04.tar.bz2
echo "export PATH=$HOME/ANTs.2.1.0.Debian-Ubuntu_X64:\\$PATH" >> .bashrc
echo "export PATH=$HOME/ANTs.2.1.0.Debian-Ubuntu_X64:\\$PATH" >> .env
rm -rf Linux_Ubuntu14.04.tar.bz2
fi
sudo sh -c 'echo "[SeatDefaults]
user-session=LXDE
autologin-user=vagrant
autologin-user-timeout=0" >> /etc/lightdm/lightdm.conf'
echo 'export FSLDIR=/usr/share/fsl/5.0' >> .bashrc
echo ". /usr/share/fsl/5.0/etc/fslconf/fsl.sh" >> .bashrc
echo "export FMRIDATADIR=$HOME/data" >> .bashrc
if [ ! -d $HOME/R_libs ]
then
mkdir $HOME/R_libs
echo "export R_LIBS_USER=$HOME/R_libs" >> .bashrc
echo "export R_LIBS_USER=$HOME/R_libs" >> .env
fi
# get example data
if [ ! -d $HOME/data ]
then
mkdir $HOME/data
fi
if [ ! -d $HOME/data/ds003 ]
then
echo "getting ds003 data"
wget --quiet http://openfmri.s3.amazonaws.com/tarballs/ds003_raw.tgz -O $HOME/data/ds003_raw.tgz -nv
tar zxvf $HOME/data/ds003_raw.tgz -C $HOME/data/
rm -rf $HOME/data/ds003_raw.tgz
fi
if [ ! -d $HOME/data/ds031 ]
then
echo "getting ds031 data"
wget --quiet https://s3.amazonaws.com/openfmri/ds031/ds031_example_data.tgz -O $HOME/data/ds031_example.tgz -nv
tar zxvf $HOME/data/ds031_example.tgz -C $HOME/data/
rm -rf $HOME/data/ds031_example.tgz
fi
# get this repo
if [ ! -d $HOME/fmri-analysis-vm ]
then
git clone https://github.com/poldrack/fmri-analysis-vm
fi
sudo apt-get clean -y
sudo apt-get autoclean -y
sudo apt-get autoremove -y
sudo VBoxClient --display -d
sudo VBoxClient --clipboard -d
SCRIPT
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
config.ssh.forward_x11 = true
config.vm.box = "ubuntu/trusty64"
config.vm.provider :virtualbox do |vb|
vb.customize ["modifyvm", :id, "--ioapic", "on"]
vb.customize ["modifyvm", :id, "--memory", "5120"]
vb.customize ["modifyvm", :id, "--cpus", "2"]
vb.customize ["setextradata", :id, "GUI/MaxGuestResolution", "any"]
vb.customize ["modifyvm", :id, "--natdnshostresolver1", "on"]
vb.customize ["modifyvm", :id, "--natdnsproxy1", "on"]
vb.customize ["modifyvm", :id, "--nictype1", "virtio"]
vb.customize ["modifyvm", :id, "--vram", "64"]
vb.gui = true
vb.name = "fmri-analysis"
end
config.vm.provision "shell", :privileged => false, inline: $script
config.push.define "atlas" do |push|
push.app = "poldracklab/fmri-analysis"
end
end