Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Fall 5
Description
Situation: There are several steps in order to fetch Kaushik's htsjdk-igb changes from his branch and then to create and deploy the artifact.
Task:
- Fetch Kaushik's branch. Kaushik's branch (igb_main-3.0.0) is created from a fork of htsjdk tag 3.0.0. Github will not allow Kaushik to create a pull request to an "empty" branch. We think the easiest solution would be for Dr. Loraine to clone the lorainelab htsjdk-igb repo on her local machine, then fetch Kaushik's branch and then push it to the lorainelab htsjdk-igb repo. For example:
- Clone the lorainelab htsjdk-igb repo:
git clone https://github.com/lorainelab/htsjdk-igb.git
- Fetch Kaushik's branch:
git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb-3.0.0
- Note that we are changing the name of Kaushik's branch to igb-3.0.0 so that it is in line with the current branch name convention of htsjdk-igb
- Push Kaushik's branch:
git push origin igb-3.0.0
- Clone the lorainelab htsjdk-igb repo:
- Build the igb-3.0.0 htsjdk-igb artifact.
- Checkout the igb-3.0.0 branch:
git checkout igb-3.0.0
- Run:
gradle jar
- A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
- Checkout the igb-3.0.0 branch:
- Deploy the artifact to https://nexus.bioviz.org/
Once the artifact has been deployed we will need to update the bigwig repo (see IGBF-3465). Kaushik will then need to create a pull request from his IGB branch (see IGBF-3464).
Loraine Lab repository lorainelab/htsjdk-igb.git master branch is now up-to-date with upstream samtools/htsjdk.git master branch.