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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| name: Reusable deploy Docker python-notebook | ||
| run-name: 'Run deploy Docker python-notebook ${{ inputs.branch }} by @${{ github.actor }}' | ||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| branch: | ||
| description: "The branch, tag or SHA of the source code to build docker." | ||
| type: string | ||
| required: true | ||
| tag: | ||
| description: "The tag for the new docker." | ||
| type: string | ||
| required: true | ||
| hadoop: | ||
| type: string | ||
| description: 'Hadoop flavour. Any of: [hdp3.1, hdi5.1, emr6.1, emr6.13]' | ||
| required: false | ||
| default: "hdp3.1" | ||
| pyopencga_version: | ||
| type: string | ||
| description: 'PyOpenCGA version.' | ||
| required: true | ||
|
|
||
| jobs: | ||
| build: | ||
| name: Build Java app | ||
| runs-on: ubuntu-22.04 | ||
| outputs: | ||
| version: ${{ steps.get_project_version.outputs.version }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: '10' | ||
| ref: "${{ inputs.branch }}" | ||
| - name: Set up JDK 8 | ||
| uses: actions/setup-java@v4 | ||
| with: | ||
| distribution: 'temurin' | ||
| java-version: '8' | ||
| cache: 'maven' | ||
| - name: Install dependencies branches | ||
| run: | | ||
| if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then | ||
| chmod +x ./.github/workflows/scripts/get_same_branch.sh | ||
| ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }} ${{ inputs.hadoop }} | ||
| fi | ||
| - name: Maven Build (skip tests) | ||
| run: mvn -T 2 clean install -DskipTests | ||
| - uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: build-folder | ||
| path: build | ||
|
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||
| deploy-docker-python-notebook: | ||
| uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop | ||
| needs: build | ||
| with: | ||
| cli: python3 ./build/cloud/docker/docker-build.py push --images python-notebook --tag ${{ inputs.tag }} --docker-build-args "-e VERSION=${{ inputs.pyopencga_version }}" | ||
| secrets: inherit |
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@@ -6,19 +6,13 @@ OpenCGA constitutes the big data analysis component of [OpenCB](http://www.openc | |
| ### Documentation | ||
| You can find OpenCGA documentation and tutorials at: https://github.com/opencb/opencga/wiki. | ||
|
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||
| ### Issues Tracking | ||
| You can report bugs or request new features at [GitHub issue tracking](https://github.com/opencb/opencga/issues). | ||
| ### Feedback and Feature Requests | ||
| Found a bug or have an idea for a new feature? Let us know at zettagenomics.com/academic. | ||
|
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||
| ### Release Notes and Roadmap | ||
| Releases notes are available at [GitHub releases](https://github.com/opencb/opencga/releases). | ||
|
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| Roadmap is available at [GitHub milestones](https://github.com/opencb/opencga/milestones). You can report bugs or request new features at [GitHub issue tracking](https://github.com/opencb/opencga/issues). | ||
|
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| ### Versioning | ||
| OpenCGA is versioned following the rules from [Semantic versioning](https://semver.org/). | ||
| Releases notes are available at https://zettagenomics.com/release-notes/ | ||
|
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||
| ### Maintainers | ||
| We recommend to contact OpenCGA developers by writing to OpenCB mailing list [email protected]. Current main developers and maintainers are: | ||
| * Ignacio Medina ([email protected]) (_Founder and Project Leader_) | ||
| * Jacobo Coll ([email protected]) | ||
| * Pedro Furio ([email protected]) | ||
|
|
@@ -33,7 +27,7 @@ We recommend to contact OpenCGA developers by writing to OpenCB mailing list ope | |
| * Franscisco Salavert ([email protected]) | ||
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| ##### Contributing | ||
| OpenCGA is an open-source and collaborative project. We appreciate any help and feedback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features or even fixing bugs. | ||
| OpenCGA is an open-source and collaborative project. We appreciate any help and feedback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features, or even fix bugs. | ||
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| # How to build | ||
|
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||
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opencga-analysis/src/main/java/org/opencb/opencga/analysis/file/AssociateAlignmentFiles.java
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| package org.opencb.opencga.analysis.file; | ||
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| import org.opencb.opencga.analysis.tools.OpenCgaToolScopeStudy; | ||
| import org.opencb.opencga.core.models.common.Enums; | ||
| import org.opencb.opencga.core.tools.annotations.Tool; | ||
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| @Tool(id = AssociateAlignmentFiles.ID, resource = Enums.Resource.FILE, type = Tool.Type.OPERATION, | ||
| description = "Automatically associate alignment files with its index and coverage files.", priority = Enums.Priority.LOW) | ||
| public class AssociateAlignmentFiles extends OpenCgaToolScopeStudy { | ||
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| public final static String ID = "associate-alignment-files"; | ||
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| @Override | ||
| protected void run() throws Exception { | ||
| catalogManager.getFileManager().associateAlignmentFiles(getStudyFqn(), token); | ||
| } | ||
|
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| } |
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