-
Notifications
You must be signed in to change notification settings - Fork 42
168 lines (168 loc) · 8.46 KB
/
ensembl-production.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
name: Ensembl/ensembl-production
on:
push:
branches:
- "**/*"
pull_request:
schedule:
- cron: "0 0 * * 1"
jobs:
test:
runs-on: ubuntu-latest
steps:
- name: checkout
uses: actions/[email protected]
- uses: shogo82148/[email protected]
with:
perl-version: "${{ matrix.perl }}"
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
- run: cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
- run: export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
- run: cpanm --sudo -v --installdeps --notest .
- run: cpanm --sudo -n Devel::Cover::Report::Coveralls
- run: cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf
- run: mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
- run: "./travisci/harness.sh"
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
strategy:
matrix:
perl:
- '5.14'
- '5.26.2'
include:
- COVERALLS: 'true'
DB: mysql
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'
env:
COVERALLS: "${{ matrix.COVERALLS }}"
DB: "${{ matrix.DB }}"
MYSQL_ROOT_PASSWORD: "ensembl"
test_2:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: 3.7.6
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: pip install -r requirements-test.txt
- run: pip install -e .
- run: pytest src/python/test
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'
test_3:
runs-on: ubuntu-latest
env:
COVERALLS: 'true'
DB: mysql
steps:
- name: checkout
uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: 3.8
- run: apt-get update && apt-get -y install unzip sendmail graphviz emboss
- run: git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
- run: export PATH=$PATH:$PWD/ensembl-git-tools/bin
- run: export ENSEMBL_BRANCH=master
- run: export SECONDARY_BRANCH=main
- run: echo "TRAVIS_BRANCH=${{ github.ref }}"
- run: if [[ ${{ github.ref }} =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=${{ github.ref }}; export SECONDARY_BRANCH=${{ github.ref }}; fi
- run: echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
- run: echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
- run: git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
- run: git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
- run: git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
- run: git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
- run: cd htslib
- run: make
- run: export HTSLIB_DIR=$(pwd -P)
- run: cd ..
- run: pip install -r requirements-test.txt
- run: pip install -e .
- run: pytest src/python/test
- uses: rtCamp/[email protected]
env:
SLACK_WEBHOOK: "${{ secrets.SLACK_WEBHOOK }}"
services:
mysql:
image: mysql
env:
MYSQL_ROOT_PASSWORD: "ensembl"
MYSQL_ALLOW_EMPTY_PASSWORD: 'true'