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TASK-426 #205

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merged 3 commits into from
Mar 22, 2022
Merged

TASK-426 #205

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41cb130
tools: replace OpenCB BigWig library with databrick lib
imedina Mar 22, 2022
275b88f
cicd: add new task.yml workflow
imedina Mar 22, 2022
d3b1b5f
cicd: rename branch in task.yml
imedina Mar 22, 2022
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47 changes: 47 additions & 0 deletions .github/workflows/task.yml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
name: Push biodata develop

on:
push:
branches:
- TASK-*

jobs:
build:
uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop

sonar:
uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
needs: build
with:
sonarProjectKey: opencb_biodata
secrets:
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}

test:
name: Test biodata
runs-on: ubuntu-20.04
needs: build
steps:
- uses: actions/checkout@v2
with:
fetch-depth: '10'
- name: Set up JDK 1.8
uses: actions/setup-java@v2
with:
distribution: 'zulu'
java-version: '8'
- name: Setup Maven Action
uses: s4u/[email protected]
with:
java-version: 8
maven-version: 3.6.3
- name: Cache Maven packages
uses: actions/cache@v2
with:
path: ~/.m2/repository
key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
restore-keys: ${{ runner.os }}-maven
- name: Install Samtools
run: sudo apt-get install samtools
- name: Run tests with Maven
run: mvn -T 2 clean install
9 changes: 7 additions & 2 deletions biodata-tools/pom.xml
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Expand Up @@ -50,9 +50,14 @@
<artifactId>log4j</artifactId>
<version>1.2.17</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>BigWig</groupId>-->
<!-- <artifactId>BigWig</artifactId>-->
<!-- </dependency>-->
<dependency>
<groupId>BigWig</groupId>
<artifactId>BigWig</artifactId>
<groupId>com.databricks</groupId>
<artifactId>SnpEff</artifactId>
<version>4.3.1</version>
</dependency>
<dependency>
<groupId>org.rocksdb</groupId>
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28 changes: 14 additions & 14 deletions pom.xml
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Expand Up @@ -75,11 +75,6 @@
<name>jacobo</name>
<email>[email protected]</email>
</developer>
<developer>
<id>javild</id>
<name>Javier</name>
<email>[email protected]</email>
</developer>
<developer>
<id>pfurio</id>
<name>Pedro</name>
Expand All @@ -90,6 +85,11 @@
<name>Joaquin</name>
<email>[email protected]</email>
</developer>
<developer>
<id>javild</id>
<name>Javier</name>
<email>[email protected]</email>
</developer>
<developer>
<id>julie-sullivan</id>
<name>Julie</name>
Expand All @@ -114,10 +114,10 @@
<updatePolicy>daily</updatePolicy>
</snapshots>
</repository>
<repository>
<id>opencb-ext-libs</id>
<url>http://bioinfo.hpc.cam.ac.uk/downloads/ext-libs</url>
</repository>
<!-- <repository>-->
<!-- <id>opencb-ext-libs</id>-->
<!-- <url>http://bioinfo.hpc.cam.ac.uk/downloads/ext-libs</url>-->
<!-- </repository>-->
</repositories>

<dependencyManagement>
Expand Down Expand Up @@ -199,11 +199,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>BigWig</groupId>
<artifactId>BigWig</artifactId>
<version>1.0</version>
</dependency>
<!-- <dependency>-->
<!-- <groupId>BigWig</groupId>-->
<!-- <artifactId>BigWig</artifactId>-->
<!-- <version>1.0</version>-->
<!-- </dependency>-->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
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