-
Notifications
You must be signed in to change notification settings - Fork 108
/
azure-pipelines.yml
290 lines (278 loc) · 11.7 KB
/
azure-pipelines.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
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
jobs:
- job: mac_latest_gcc
pool:
vmImage: macOS-latest
steps:
- script: |
find /usr/local/bin -lname '*/Library/Frameworks/Python.framework/*' -delete # Trying solution from https://github.com/mesonbuild/meson/blob/master/.github/workflows/macos.yml#L87-L92
sudo rm -rf /Library/Frameworks/Python.framework/
brew install --force python3 node@18 && brew unlink python3 node@18 && brew unlink python3 node@18 && brew link --overwrite python3 node@18
find /usr/local/Cellar/python* -name EXTERNALLY-MANAGED -print0 | xargs -0 rm -vf
brew update
brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@14 llvm
displayName: Install common
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.5.0/btllib-1.5.0.tar.gz
export CC=gcc-14
export CXX=g++-14
tar xzf btllib-1.5.0.tar.gz
cd btllib-1.5.0
./compile
displayName: Install btllib
- script: |
./autogen.sh
export CC=gcc-14
export CXX=g++-14
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install"
./configure CC=gcc-14 CXX=g++-14 --with-boost=/usr/local/opt/boost --with-sparsehash=/usr/local/opt/google-sparsehash --with-mpi=/usr/local/opt/openmpi --with-btllib=/Users/runner/work/1/s/btllib-1.5.0/install
make -j12 distcheck AM_CXXFLAGS=-Wno-error=dangling-reference
displayName: Compiling ABySS with gcc-14
- job:
displayName: mac_latest-compilers-clang
pool:
vmImage: 'macOS-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
displayName: Compiling ABySS
- job:
displayName: mac_clang14
pool:
vmImage: 'macOS-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck
displayName: Compiling ABySS
- job:
displayName: mac_clang13
pool:
vmImage: 'macOS-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck
displayName: Compiling ABySS with clang 13
- job:
displayName: mac_clang12
pool:
vmImage: 'macOS-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck
displayName: Compiling ABySS with clang 12
- job: linux_gcc12
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-12 g++-12
displayName: Install gcc-12
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-12
export CXX=g++-12
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-12 CXX=g++-12 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-12 CXX=g++-12 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-12
- job: linux_gcc11
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-11 g++-11
displayName: Install gcc-11
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-11
export CXX=g++-11
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-11 CXX=g++-11 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-11 CXX=g++-11 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-11
- job: linux_gcc10
pool:
vmImage: ubuntu-20.04
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-10 g++-10
displayName: Install gcc-10
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-10
export CXX=g++-10
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-10 CXX=g++-10 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-10 CXX=g++-10 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-10
- script: |
curl https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
sudo apt-add-repository "deb http://apt.llvm.org/xenial/ llvm-toolchain-xenial-8 main"
sudo apt-get update
sudo apt-get install -y --no-install-recommends clang-format-8
sudo ln -sf clang-format-8 /usr/bin/clang-format
displayName: Install clang-format
- script: make clang-format
displayName: Run clang-format
- job: linux_gcc9
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-9 g++-9
displayName: Install gcc-9
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.7.2/btllib-1.7.2.tar.gz
tar xzf btllib-1.7.2.tar.gz
cd btllib-1.7.2
export CC=gcc-9
export CXX=g++-9
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-9 CXX=g++-9 --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install"
./configure CC=gcc-9 CXX=g++-9 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.7.2/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-9
- job: linux_gcc8
pool:
vmImage: ubuntu-latest
steps:
- script: |
sudo apt-get update -qq
sudo apt-get install -qq software-properties-common
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu focal main universe security"
sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu focal-updates main universe restricted"
sudo apt-get update -qq
sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc
displayName: Install common
- script: sudo apt-get install -qq gcc-8 g++-8
displayName: Install gcc-8
- script: |
wget https://github.com/bcgsc/btllib/releases/download/v1.6.0/btllib-1.6.0.tar.gz
tar xzf btllib-1.6.0.tar.gz
cd btllib-1.6.0
export CC=gcc-8
export CXX=g++-8
./compile
displayName: Install btllib
- script: |
./autogen.sh
export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8 --with-btllib=/home/vsts/work/1/s/btllib-1.6.0/install"
./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi --with-btllib=/home/vsts/work/1/s/btllib-1.6.0/install
make -j12 distcheck
displayName: Compiling ABySS with gcc-8
- job:
displayName: linux_gcc-latest
pool:
vmImage: 'ubuntu-latest'
steps:
- script: echo "##vso[task.prependpath]$CONDA/bin"
displayName: Add conda to PATH
- script: conda create --yes --quiet --name abyss_CI
displayName: Create Anaconda environment
- script: |
source activate abyss_CI
conda install --yes -c conda-forge mamba python=3.9
mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi util-linux perl btllib pandoc
displayName: Install dependencies
- script: |
source activate abyss_CI
./autogen.sh
./configure
make -j12 distcheck AM_CXXFLAGS=-Wall CXXFLAGS='-pthread'
displayName: Compiling ABySS with gcc