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
|
# For most projects, this workflow file will not need changing; you simply need
# to commit it to your repository.
#
# You may wish to alter this file to override the set of languages analyzed,
# or to provide custom queries or build logic.
#
# ******** NOTE ********
# We have attempted to detect the languages in your repository. Please check
# the `language` matrix defined below to confirm you have the correct set of
# supported CodeQL languages.
#
name: "CodeQL"
on:
push:
branches: [ master, develop ]
paths:
- '**/CMakeLists.txt'
- 'pom.xml'
- 'src/main/**'
- 'src/resources/**'
- '.github/resources/codeql-config.yml'
- '.github/workflows/codeql.yml'
pull_request:
branches: [ master, develop ]
paths:
- '**/CMakeLists.txt'
- 'pom.xml'
- 'src/main/**'
- 'src/resources/**'
- '.github/resources/codeql-config.yml'
- '.github/workflows/codeql.yml'
env:
PREREQS_ENV: ${{github.workspace}}/prereqs.sh
PREREQS_INSTALL_DIR: ${{github.workspace}}/prereqs
CMAKE_INSTALL_PREFIX: ${{github.workspace}}/install
GENOMICSDB_BUILD_DIR: ${{github.workspace}}/build
jobs:
analyze:
name: Analyze
runs-on: ubuntu-20.04
permissions:
actions: read
contents: read
security-events: write
strategy:
fail-fast: false
# CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
# Learn more about CodeQL language support at https://git.io/codeql-language-support
steps:
- uses: actions/checkout@v4
- uses: actions/setup-java@v4
with:
distribution: 'temurin'
java-package: jdk
java-version: '17'
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
config-file: ./.github/resources/codeql-config.yml
languages: cpp, java
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.
# queries: ./path/to/local/query, your-org/your-repo/queries@main
- name: Cache built prerequisites for ubuntu
uses: actions/cache@v4
with:
path: |
${{env.PREREQS_INSTALL_DIR}}
~/.m2/repository
~/awssdk-install
~/gcssdk-install
~/protobuf-install
key: ubuntu-codeql-cache-prereqs-v1
- name: Build GenomicsDB
shell: bash
run: |
$GITHUB_WORKSPACE/.github/scripts/cleanup_hosts.sh
echo "Install Prerequisites for Linux.."
pushd $GITHUB_WORKSPACE/scripts/prereqs
sudo INSTALL_PREFIX=$PREREQS_INSTALL_DIR PREREQS_ENV=$PREREQS_ENV ./install_prereqs.sh
popd
echo "Install prerequisites for Linux DONE"
source $PREREQS_ENV
cmake $GITHUB_WORKSPACE -DCMAKE_PREFIX_PATH=$PREREQS_INSTALL_DIR -DBUILD_JAVA=1 -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX
make -j4
make install
rm -fr dependencies/ src/test/ test/
# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
# - name: Autobuild
# uses: github/codeql-action/autobuild@v1
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v3
|
