[IGBF-3484] Update htsjdk-igb to 3.0.0 - JIRA UNCC

Nowlan Freese created issue - 31/Oct/23 10:55 AM

Nowlan Freese made changes - 31/Oct/23 10:55 AM

Field	Original Value	New Value
Epic Link		~~IGBF-3467~~ [ 22628 ]

Nowlan Freese made changes - 31/Oct/23 10:55 AM

Link

This issue relates to ~~IGBF-3464~~ [ ~~IGBF-3464~~ ]

Nowlan Freese made changes - 31/Oct/23 11:02 AM

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.

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}

Nowlan Freese made changes - 31/Oct/23 11:21 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to https://nexus.bioviz.org/*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 31/Oct/23 11:22 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to https://nexus.bioviz.org/*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 31/Oct/23 11:22 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
*** A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 31/Oct/23 11:22 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
*** A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 31/Oct/23 11:22 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 31/Oct/23 11:23 AM

Summary

Get new htsjdk changes and deploy artifact

Get new htsjdk-igb changes and deploy artifact

Ann Loraine made changes - 31/Oct/23 12:19 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Ann Loraine added a comment - 31/Oct/23 1:43 PM - edited

Loraine Lab repository lorainelab/htsjdk-igb.git master branch is now up-to-date with upstream samtools/htsjdk.git master branch.

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Ann Loraine added a comment - 31/Oct/23 1:43 PM - edited Loraine Lab repository lorainelab/htsjdk-igb.git master branch is now up-to-date with upstream samtools/htsjdk.git master branch.

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Ann Loraine added a comment - 31/Oct/23 1:59 PM

Request for Nowlan Freese and Kaushik Gopu:

Is it OK with you if I call this new branch "igb-3.0.0" instead of "igb_main-3.0.0".

Also, a question:

Can you let me know the name of branch you mentioned during the scrum that Charan had made that you said doesn't exist in lorainelab/htsjdk-igb.git?

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Ann Loraine added a comment - 31/Oct/23 1:59 PM Request for Nowlan Freese and Kaushik Gopu : Is it OK with you if I call this new branch "igb-3.0.0" instead of "igb_main-3.0.0". Also, a question: Can you let me know the name of branch you mentioned during the scrum that Charan had made that you said doesn't exist in lorainelab/htsjdk-igb.git?

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Nowlan Freese added a comment - 31/Oct/23 2:23 PM - edited

[~aloraine] - replies to questions above:

I think igb-3.0.0 would be good as it matches the current convention on the lorainelab htsjdk-igb branch name.
Charan's branch - https://github.com/VallapuCharan/htsjdk-igb/tree/igb-2.16.3
1. UPDATE - Looks like the lorainelab repo does have 2.16.3 (see https://github.com/lorainelab/htsjdk-igb/tree/igb-2.16.3). Did not see the 2.16.3 branch as 2.16.2 was set as the default.

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Nowlan Freese added a comment - 31/Oct/23 2:23 PM - edited [~aloraine] - replies to questions above: I think igb-3.0.0 would be good as it matches the current convention on the lorainelab htsjdk-igb branch name. Charan's branch - https://github.com/VallapuCharan/htsjdk-igb/tree/igb-2.16.3 UPDATE - Looks like the lorainelab repo does have 2.16.3 (see https://github.com/lorainelab/htsjdk-igb/tree/igb-2.16.3 ). Did not see the 2.16.3 branch as 2.16.2 was set as the default.

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Ann Loraine added a comment - 31/Oct/23 3:06 PM

Thank you for the clarification Nowlan Freese.
New branch from Kaushik Gopu repository pushed to lorainelab/htsjdk-igb.

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Ann Loraine added a comment - 31/Oct/23 3:06 PM Thank you for the clarification Nowlan Freese . New branch from Kaushik Gopu repository pushed to lorainelab/htsjdk-igb.

Nowlan Freese made changes - 01/Nov/23 10:08 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb_main-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb_main-3.0.0{code}
# *Build the igb_main-3.0.0 htsjdk-igb artifact*.
## Checkout the igb_main-3.0.0 branch: {code}git checkout igb_main-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb-3.0.0{code}
# *Build the igb-3.0.0 htsjdk-igb artifact*.
## Checkout the igb-3.0.0 branch: {code}git checkout igb-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

Nowlan Freese made changes - 01/Nov/23 10:09 AM

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb-3.0.0{code}
## Push Kaushik's branch: {code}git push origin igb-3.0.0{code}
# *Build the igb-3.0.0 htsjdk-igb artifact*.
## Checkout the igb-3.0.0 branch: {code}git checkout igb-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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|https://github.com/kaushik-gopu1998/htsjdk-kg] (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|https://github.com/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: {code}git clone https://github.com/lorainelab/htsjdk-igb.git{code}
## Fetch Kaushik's branch: {code}git fetch https://github.com/kaushik-gopu1998/htsjdk-kg igb_main-3.0.0:igb-3.0.0{code}
### 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: {code}git push origin igb-3.0.0{code}
# *Build the igb-3.0.0 htsjdk-igb artifact*.
## Checkout the igb-3.0.0 branch: {code}git checkout igb-3.0.0{code}
## Run: {code}gradle jar{code}
## A folder named build will appear after running the above command. Look for htsjdk-igb-3.0.0.jar in build/libs folder.
# *Deploy the artifact to [https://nexus.bioviz.org/|https://nexus.bioviz.org/]*

Once the artifact has been deployed we will need to update the [bigwig|https://bitbucket.org/lorainelab/bigwig/src/master/] repo (see ~~IGBF-3465~~). Kaushik will then need to create a pull request from his [IGB branch|https://bitbucket.org/kaushik-gopu/kgopu_integrated-genome-browser/branch/IGBF-3464] (see ~~IGBF-3464~~).

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Ann Loraine added a comment - 01/Nov/23 11:17 AM - edited

Built the new jar, following the instructions in the README.

Unpacked the newly build jar file and checked the OSGI meta-data in the MANIFEST.

However, the bundle symbolic name is listed as htsjdk, not htsjdk-igb, as expected.

Please see https://nexus.bioviz.org/#browse/browse:maven-releases:htsjdk-igb to observe the OSGi metadata in older versions of the bundle.

Also note that we need to also provide javadoc and sources in the Nexus repository, similar to what we did before.

Kaushik Gopu - can you take a look? Please see if you can figure out how we built zip files for the javadocs and the source zip file for release on the nexus maven repository.

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Ann Loraine added a comment - 01/Nov/23 11:17 AM - edited Built the new jar, following the instructions in the README. Unpacked the newly build jar file and checked the OSGI meta-data in the MANIFEST. However, the bundle symbolic name is listed as htsjdk, not htsjdk-igb, as expected. Please see https://nexus.bioviz.org/#browse/browse:maven-releases:htsjdk-igb to observe the OSGi metadata in older versions of the bundle. Also note that we need to also provide javadoc and sources in the Nexus repository, similar to what we did before. Kaushik Gopu - can you take a look? Please see if you can figure out how we built zip files for the javadocs and the source zip file for release on the nexus maven repository.

Ann Loraine made changes - 01/Nov/23 11:21 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 01/Nov/23 11:22 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 01/Nov/23 11:22 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 01/Nov/23 11:22 AM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 01/Nov/23 4:14 PM

To deploy the new code to our Nexus maven repository, we need to include deployment code in the build.gradle script.

Please see: https://github.com/lorainelab/htsjdk-igb/blame/igb-2.16.3/build.gradle and function named uploadArchives.

This uploadArchives code needs to be added to the new igb-3.0.0 build.gradle file. Once it's added, I can use it to deploy the jar file, the javadocs, etc to the maven repository.

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Ann Loraine added a comment - 01/Nov/23 4:14 PM To deploy the new code to our Nexus maven repository, we need to include deployment code in the build.gradle script. Please see: https://github.com/lorainelab/htsjdk-igb/blame/igb-2.16.3/build.gradle and function named uploadArchives . This uploadArchives code needs to be added to the new igb-3.0.0 build.gradle file. Once it's added, I can use it to deploy the jar file, the javadocs, etc to the maven repository.

Ann Loraine made changes - 01/Nov/23 4:15 PM

Assignee

Kaushik Gopu [ kgopu ]

Nowlan Freese made changes - 02/Nov/23 10:10 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Kaushik Gopu added a comment - 02/Nov/23 10:56 AM

Added uploadArchives code to the build.gradle
pull request submitted to the upstream repository (lorainelab-igb)

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Kaushik Gopu added a comment - 02/Nov/23 10:56 AM Added uploadArchives code to the build.gradle pull request submitted to the upstream repository (lorainelab-igb)

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Ann Loraine added a comment - 02/Nov/23 3:48 PM

I have merged the new code and rebuilt the jar file. The bundle symbolic name is still not htsjdk-igb:

Manifest-Version: 1.0
Bnd-LastModified: 1698954380474
Bundle-Description: htsjdk for IGB
Bundle-DocURL: https://github.com/lorainelab/htsjdk
Bundle-ManifestVersion: 2
Bundle-Name: htsjdk for IGB
Bundle-SymbolicName: htsjdk
Bundle-Vendor: Loraine Lab
Bundle-Version: 3.0.0

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Ann Loraine added a comment - 02/Nov/23 3:48 PM I have merged the new code and rebuilt the jar file. The bundle symbolic name is still not htsjdk-igb: Manifest-Version: 1.0 Bnd-LastModified: 1698954380474 Bundle-Description: htsjdk for IGB Bundle-DocURL: https: //github.com/lorainelab/htsjdk Bundle-ManifestVersion: 2 Bundle-Name: htsjdk for IGB Bundle-SymbolicName: htsjdk Bundle-Vendor: Loraine Lab Bundle-Version: 3.0.0

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Ann Loraine added a comment - 02/Nov/23 4:15 PM

Kaushik Gopu - please investigate. How do we ensure that the correct bundle symbolic name gets used?

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Ann Loraine added a comment - 02/Nov/23 4:15 PM Kaushik Gopu - please investigate. How do we ensure that the correct bundle symbolic name gets used?

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Kaushik Gopu added a comment - 02/Nov/23 4:23 PM - edited

Sure, [~aloraine]. I am on it. There isn't any property specifying Bundle-Symbolic name under bundle properties. I wonder whether it was appearing for previous versions. Can you tell where you are checking this bundle information.

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Kaushik Gopu added a comment - 02/Nov/23 4:23 PM - edited Sure, [~aloraine] . I am on it. There isn't any property specifying Bundle-Symbolic name under bundle properties. I wonder whether it was appearing for previous versions. Can you tell where you are checking this bundle information.

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Ann Loraine added a comment - 02/Nov/23 5:21 PM

Answering Kaushik Gopu:

The bundle symbolic name is listed in the jar file manifest. Unzip the jar file. You will see a folder named META-INF. Inside that folder there is a file named MANIFEST.MF.

An OSGi bundle has attributes with prefix "Bundle". The "Bundle-SymbolicName" is listed as htsjdk and not htsjdk-igb. However, the older bundles we deployed previously have the correct symbolic name of "htsjdk-igb."
For example, see:
https://nexus.bioviz.org/#browse/browse:maven-releases:htsjdk-igb%2Fhtsjdk-igb%2F2.16.3

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Ann Loraine added a comment - 02/Nov/23 5:21 PM Answering Kaushik Gopu : The bundle symbolic name is listed in the jar file manifest. Unzip the jar file. You will see a folder named META-INF. Inside that folder there is a file named MANIFEST.MF. An OSGi bundle has attributes with prefix "Bundle". The "Bundle-SymbolicName" is listed as htsjdk and not htsjdk-igb. However, the older bundles we deployed previously have the correct symbolic name of "htsjdk-igb." For example, see: https://nexus.bioviz.org/#browse/browse:maven-releases:htsjdk-igb%2Fhtsjdk-igb%2F2.16.3

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Ann Loraine added a comment - 03/Nov/23 9:45 AM

Suggestion: Check out the older branches and build all the artifacts using gradlew - the javadoc, the source zip file, the compiled code jar file. Do this to check the build.
Next, unpack the compiled code jar file and inspect the MANIFEST.MF file packaged with it. Check: Are the OSGi metadata fields correct, or not?
If the older build file works, then clearly something is different about the newer build file that needs to be fixed.
Then, examine the two files line by line to identify a possible difference that could explain the problem.
If no such difference can be found, then there is something about some other file in the repository that is the problem.
Then, look through the entire repository for possible configuration files.
Also, google "build osgi bundle using gradle"
One last thing: you are using a bnd plugin artifact to add the proper metadata to the MANIFEST file in order to make it a bundle. Maybe you need to configure the bnd plugin in a way that will enable it to specify the propery bundle symbolic name field.

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Ann Loraine added a comment - 03/Nov/23 9:45 AM Suggestion: Check out the older branches and build all the artifacts using gradlew - the javadoc, the source zip file, the compiled code jar file. Do this to check the build. Next, unpack the compiled code jar file and inspect the MANIFEST.MF file packaged with it. Check: Are the OSGi metadata fields correct, or not? If the older build file works, then clearly something is different about the newer build file that needs to be fixed. Then, examine the two files line by line to identify a possible difference that could explain the problem. If no such difference can be found, then there is something about some other file in the repository that is the problem. Then, look through the entire repository for possible configuration files. Also, google "build osgi bundle using gradle" One last thing: you are using a bnd plugin artifact to add the proper metadata to the MANIFEST file in order to make it a bundle. Maybe you need to configure the bnd plugin in a way that will enable it to specify the propery bundle symbolic name field.

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Kaushik Gopu added a comment - 06/Nov/23 11:31 AM - edited

After updating the root project name to htsjdk-igb in settings.gradle file, the bundle symbolic name appears in the manifest file.

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Kaushik Gopu added a comment - 06/Nov/23 11:31 AM - edited After updating the root project name to htsjdk-igb in settings.gradle file, the bundle symbolic name appears in the manifest file.

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Kaushik Gopu added a comment - 06/Nov/23 4:09 PM - edited

[~aloraine], Pull requested has been submitted to htsjdk-igb repository.

You should able to see the Bundle Symbolic name in the manifest file
Updated the instructions in README under the Build Artifact section and added the Deploy Artifact section to install artifacts locally and remotely

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Kaushik Gopu added a comment - 06/Nov/23 4:09 PM - edited [~aloraine] , Pull requested has been submitted to htsjdk-igb repository. You should able to see the Bundle Symbolic name in the manifest file Updated the instructions in README under the Build Artifact section and added the Deploy Artifact section to install artifacts locally and remotely

Nowlan Freese made changes - 07/Nov/23 10:59 AM

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Nowlan Freese added a comment - 07/Nov/23 12:02 PM

I built the htsjdk-igb igb-3.0.0-bundle-fix branch locally. The manifest shows Bundle-SymbolicName: htsjdk-igb

Ready for pull request.

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Nowlan Freese added a comment - 07/Nov/23 12:02 PM I built the htsjdk-igb igb-3.0.0-bundle-fix branch locally. The manifest shows Bundle-SymbolicName: htsjdk-igb Ready for pull request.

Nowlan Freese made changes - 07/Nov/23 12:02 PM

Assignee

Kaushik Gopu [ kgopu ]

Nowlan Freese made changes - 07/Nov/23 12:03 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 07/Nov/23 12:03 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 07/Nov/23 12:03 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

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Nowlan Freese added a comment - 07/Nov/23 12:04 PM - edited

[~aloraine] - Here is Kaushik's pull request: https://github.com/lorainelab/htsjdk-igb/pull/9

Note that this pull request also includes edits to the readme from ~~IGBF-3485~~ as separate commits.

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Nowlan Freese added a comment - 07/Nov/23 12:04 PM - edited [~aloraine] - Here is Kaushik's pull request: https://github.com/lorainelab/htsjdk-igb/pull/9 Note that this pull request also includes edits to the readme from IGBF-3485 as separate commits.

Nowlan Freese made changes - 07/Nov/23 12:04 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Nowlan Freese made changes - 08/Nov/23 10:00 AM

Summary

Get new htsjdk-igb changes and deploy artifact

Update htsjdk-igb to 3.0.0

Ann Loraine made changes - 09/Nov/23 1:43 PM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 09/Nov/23 1:43 PM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

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Ann Loraine added a comment - 09/Nov/23 1:46 PM

PR is merged. Ready for testing.

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Ann Loraine added a comment - 09/Nov/23 1:46 PM PR is merged. Ready for testing.

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Nowlan Freese added a comment - 10/Nov/23 9:46 AM - edited

Tested on Mac

Fetched the igb-3.0.0 branch from lorainelab htsjdk-igb.
Ran ./gradlew clean build -x test. The jar, sources, and javadoc files all appeared in the build > libs folder.
In the MANIFEST.MF file the Bundle-SymbolicName was listed as htsjdk-igb
Ran gradle install. The htsjdk-igb 3.0.0 files were installed into my local .m2 repository.
Using Kaushik's ~~IGBF-3464~~ branch I was able to build and run IGB (the branch specifies htsjdk-igb version 3.0.0).

Closing ticket.

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Nowlan Freese added a comment - 10/Nov/23 9:46 AM - edited Tested on Mac Fetched the igb-3.0.0 branch from lorainelab htsjdk-igb. Ran ./gradlew clean build -x test . The jar, sources, and javadoc files all appeared in the build > libs folder. In the MANIFEST.MF file the Bundle-SymbolicName was listed as htsjdk-igb Ran gradle install . The htsjdk-igb 3.0.0 files were installed into my local .m2 repository. Using Kaushik's IGBF-3464 branch I was able to build and run IGB (the branch specifies htsjdk-igb version 3.0.0). Closing ticket.

Nowlan Freese made changes - 10/Nov/23 9:47 AM

Assignee

Kaushik Gopu [ kgopu ]

Nowlan Freese made changes - 10/Nov/23 9:47 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Nowlan Freese made changes - 10/Nov/23 9:47 AM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Nowlan Freese made changes - 10/Nov/23 4:31 PM

Link

This issue relates to ~~IGBF-3490~~ [ ~~IGBF-3490~~ ]

Nowlan Freese made changes - 07/Feb/24 1:46 PM

Fix Version/s

10.0.0 Major Release [ 10900 ]

Nowlan Freese made changes - 07/Feb/24 1:46 PM

Issue Type

Task [ 3 ]

Improvement [ 4 ]

Nowlan Freese made changes - 27/Mar/24 2:00 PM

Link

This issue relates to ~~IGBF-3671~~ [ ~~IGBF-3671~~ ]

Update htsjdk-igb to 3.0.0

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