-
Notifications
You must be signed in to change notification settings - Fork 6
306 lines (256 loc) · 8.51 KB
/
main.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
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
name: run-exemplary-workflow
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
run-pydoit:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
environment-file: exemplary_workflow/source/envs/default_env.yaml
miniforge-version: latest
activate-environment: exemplary_workflow
- name: run-workflow
shell: bash -l {0}
run: |
conda install --channel conda-forge doit=0.33.1
cd $GITHUB_WORKSPACE/exemplary_workflow/pydoit
doit
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/pydoit/paper.pdf
retention-days: 1
if-no-files-found: error
run-cwl:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
environment-file: exemplary_workflow/source/envs/default_env.yaml
miniforge-version: latest
activate-environment: exemplary_workflow
- name: run-workflow
shell: bash -l {0}
run: |
conda install --channel conda-forge cwltool
cd $GITHUB_WORKSPACE/exemplary_workflow/cwl
cwltool wf_run_exemplary_wf.cwl
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/cwl/paper.pdf
retention-days: 1
if-no-files-found: error
run-nextflow:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-version: latest
activate-environment: exemplary_workflow
- name: run-workflow
shell: bash -l {0}
run: |
conda install --channel bioconda nextflow=21.04.0
cd $GITHUB_WORKSPACE/exemplary_workflow/nextflow
nextflow run exemplarywf.nf
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/nextflow/paper.pdf
retention-days: 1
if-no-files-found: error
run-snakemake:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-version: latest
activate-environment: exemplary_workflow
channels: conda-forge,bioconda
channel-priority: strict
- name: run-workflow
shell: bash -l {0}
run: |
conda install snakemake
cd $GITHUB_WORKSPACE/exemplary_workflow/snakemake
snakemake --cores 1 --use-conda --conda-frontend conda ./paper.pdf
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/snakemake/paper.pdf
retention-days: 1
if-no-files-found: error
run-kadistudio:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
environment-file: exemplary_workflow/source/envs/default_env.yaml
miniforge-version: latest
activate-environment: exemplary_workflow
- name: run-workflow
shell: bash -l -i {0}
run: |
bash $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/install_components.sh
mkdir $GITHUB_WORKSPACE/run
process_engine run $GITHUB_WORKSPACE/exemplary_workflow/kadistudio/exemplary_workflow.flow -p $GITHUB_WORKSPACE/run
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/kadistudio/paper.pdf
retention-days: 1
if-no-files-found: error
run-aiida:
runs-on: ubuntu-latest
services:
postgres:
image: postgres:10
env:
POSTGRES_DB: test_aiida
POSTGRES_PASSWORD: ''
POSTGRES_HOST_AUTH_METHOD: trust
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 5432:5432
rabbitmq:
image: rabbitmq:3.8.14
ports:
- 5672:5672
slurm:
image: xenonmiddleware/slurm:17
ports:
- 5001:22
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: install-system-dependencies
run: |
sudo apt update
sudo apt install postgresql graphviz
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
environment-file: exemplary_workflow/source/envs/default_env.yaml
miniforge-version: latest
activate-environment: exemplary_workflow
- name: install-aiida-shell
# the shell directive is necessary to properly activate the shell
# see https://github.com/marketplace/actions/setup-miniconda
shell: bash -l {0}
run: |
pip install "aiida-core>=2.0,<2.1" "aiida-shell==0.2.0"
- name: setup-aiida-profile
shell: bash -l {0}
run: |
verdi quicksetup --non-interactive --profile default --email aiida@localhost --first-name Giuseppe --last-name Verdi --institution Khedivial --db-backend psql_dos
- name: run-workflow
working-directory: exemplary_workflow/aiida
shell: bash -l {0}
run:
./exemplary_workflow.py
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/aiida/paper.pdf
retention-days: 1
if-no-files-found: error
run-gwl:
runs-on: ubuntu-latest
steps:
- name: Install Guix
id: install-guix
uses: PromyLOPh/guix-install-action@v1
with:
channels: |-
(list (channel
(name 'guix)
(url "https://git.savannah.gnu.org/git/guix.git")
(branch "master")
(commit
"8e54584d4448d37ddf8ae995bb545a181ba2493c")))
- name: Install Guix Workflow Language
run: |
guix install gwl
echo "GUIX_EXTENSIONS_PATH=$HOME/.guix-profile/share/guix/extensions" >> $GITHUB_ENV
- name: checkout-repository
uses: actions/checkout@v2
- name: run-workflow
run: |
cd exemplary_workflow/gwl
guix workflow run workflow.w
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: exemplary_workflow/gwl/paper.pdf
run-pyiron:
runs-on: ubuntu-latest
steps:
- name: checkout-repository
uses: actions/checkout@v2
- name: install-basic-deps
uses: ./.github/actions/install-basic-deps
- name: setup-conda-environment
uses: conda-incubator/setup-miniconda@v2
with:
miniforge-version: latest
activate-environment: exemplary_workflow
channels: conda-forge
channel-priority: strict
- name: run-workflow
shell: bash -l {0}
run: |
conda install conda_subprocess=0.0.4 pyiron_base=0.9.6
cd $GITHUB_WORKSPACE/exemplary_workflow/pyiron
python workflow.py
- name: upload-paper-artifact
uses: actions/upload-artifact@v2
with:
name: paper
path: ./exemplary_workflow/pyiron/workflow/tectonic_hdf5/tectonic/paper.pdf
retention-days: 1
if-no-files-found: error