-
Notifications
You must be signed in to change notification settings - Fork 27
185 lines (182 loc) · 6.32 KB
/
f5c-x86_64.yml
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
182
183
184
185
name: Linux x86_64
on:
push:
branches: '**'
pull_request:
branches: '**'
env:
ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
jobs:
ubuntu_14_local_hts:
name: ubuntu 14 local hts
runs-on: ubuntu-20.04
container: ubuntu:14.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget
- name: env
run: lsb_release -a && ldd --version && gcc --version && g++ --version
- name: build
run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8
- name: test
run: make test
ubuntu_16_install_scripts:
name: Ubuntu 16 install scripts
runs-on: ubuntu-20.04
container: ubuntu:16.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: apt-get update && apt-get install -y zlib1g-dev valgrind gcc g++ autoconf automake make wget bzip2
- name: build
run: autoreconf && ./scripts/install-hdf5.sh &&./scripts/install-hts.sh && ./configure --enable-localhdf5 && make -j8
- name: test
run: make test
- name: test valgrind
run: valgrind --leak-check=full --error-exitcode=1 ./f5c call-methylation -b test/ecoli_2kb_region/reads.sorted.bam -g test/ecoli_2kb_region/draft.fa -r test/ecoli_2kb_region/reads.fasta -t 8 -K 256 -B 2M > /dev/null
ubuntu_16_pure_make:
name: Ubuntu 16 pure make
runs-on: ubuntu-20.04
container: ubuntu:16.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: apt-get update && apt-get install -y zlib1g-dev gcc g++ autoconf automake make wget bzip2
- name: build
run: make
- name: test
run: make test
ubuntu_18:
name: Ubuntu 18
runs-on: ubuntu-20.04
container: ubuntu:18.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: apt-get update && apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget bzip2
- name: build
run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8
- name: test
run: make test
ubuntu_20:
name: Ubuntu 20
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev
- name: build
run: autoreconf && ./scripts/install-hts.sh && ./configure && make -j8
- name: test
run: make test
ubuntu_22:
name: Ubuntu 22
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure --disable-hdf5 && make -j8 disable_hdf5=1
- name: test
run: test/test_slow5.sh
ubuntu_24:
name: Ubuntu 24
runs-on: ubuntu-24.04
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure --disable-hdf5 && make -j8 disable_hdf5=1
- name: test
run: test/test_slow5.sh
ubuntu_14_cuda_6_5:
name: Ubuntu 14 cuda 6.5
runs-on: ubuntu-20.04
container: ubuntu:14.04
steps:
- uses: actions/checkout@v2
- name: install packages
run: sudo apt-get update && sudo apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget
- name: env
run: lsb_release -a && ldd --version && gcc --version && g++ --version
- name: cuda repo setup
run: wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1404/x86_64/cuda-repo-ubuntu1404_7.0-28_amd64.deb && sudo dpkg -i cuda-repo-ubuntu1404_7.0-28_amd64.deb && sudo apt-get update
- name: cuda install
run: sudo apt-get install -y cuda-core-6-5 cuda-cudart-dev-6-5
- name: cuda env setup
run: sudo ln -s /usr/local/cuda-6.5/ /usr/local/cuda
- name: build
run: export PATH=/usr/local/cuda/bin:${PATH} && autoreconf && ./scripts/install-hts.sh && ./configure && make cuda=1 -j8
- name: test
run: make test || scripts/test.sh custom --disable-cuda=yes
os_x_12:
name: OSX 12
runs-on: macos-12
steps:
- uses: actions/checkout@v2
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure && make -j8
- name: test
run: make test
os_x_12_2:
name: OSX 12 hdf5 install script
runs-on: macos-12
steps:
- uses: actions/checkout@v2
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && CC=gcc CXX=g++ CFLAGS="-Wno-implicit-function-declaration" ./scripts/install-hdf5.sh && ./scripts/install-hts.sh && ./configure --enable-localhdf5 && make -j8
- name: test
run: make test
os_x_13:
name: OSX 13
runs-on: macos-13
steps:
- uses: actions/checkout@v2
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure && make -j8
- name: test
run: make test
os_x_14:
name: OSX 14
runs-on: macos-14
steps:
- uses: actions/checkout@v2
- name: install packages
run: brew install hdf5 autoconf automake
- name: build
run: autoreconf --install && ./scripts/install-hts.sh && ./configure --disable-hdf5 && make -j8
- name: test
run: test/test_slow5.sh
ubuntu_arm:
name: ubuntu arm
runs-on: ubuntu-latest
steps:
- run: docker run --rm --privileged multiarch/qemu-user-static:register --reset
- uses: docker://multiarch/ubuntu-core:arm64-bionic
with:
args: 'uname -a'
- uses: actions/checkout@v1
- uses: docker://multiarch/ubuntu-core:arm64-bionic
with:
args: >
bash -c "apt-get update &&
apt-get install -y zlib1g-dev libhdf5-dev gcc g++ autoconf automake make wget &&
ldd --version && gcc --version && g++ --version &&
autoreconf &&
./scripts/install-hts.sh &&
./configure &&
make -j8 &&
make test"