New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ADAM-540] Move to new HTSJDK release; should support Java 8. #619

Merged
merged 1 commit into from Mar 24, 2015

Conversation

Projects
None yet
5 participants
@fnothaft
Member

fnothaft commented Mar 16, 2015

Resolves #540. Moves to the new HTSJDK release which removes the Cofoja dependency that was blocking Java 8 support. A few notes:

  • I have not tested this on Java 8 as I don't have a system with Java 8 on it; @antonkulaga would you mind trying to build this?
  • I want to test this a bit further. It requires some funny shading in Hadoop-BAM; I'm optimistic that we don't need to do anything more than the funny shading, but I realize that optimism is likely wrong.
@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Mar 16, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/632/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/632/
Test PASSed.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Mar 16, 2015

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/633/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/633/
Test PASSed.

@AndreSchumacher

This comment has been minimized.

Show comment
Hide comment
@AndreSchumacher

AndreSchumacher Mar 22, 2015

Hey @fnothaft, I have been a bit out of sync but great to see that official HTSJDK artifacts are now available. I guess the optimal way would be to update Hadoop-BAM to use these then no funny shading would be required. I would need to have a look at the API changes but pull requests are of course welcome :-)

Hey @fnothaft, I have been a bit out of sync but great to see that official HTSJDK artifacts are now available. I guess the optimal way would be to update Hadoop-BAM to use these then no funny shading would be required. I would need to have a look at the API changes but pull requests are of course welcome :-)

@massie

This comment has been minimized.

Show comment
Hide comment
@massie

massie Mar 24, 2015

Member

This is good stuff, Frank. We'll move our test environment on Jenkins over the Java 8 in order to make sure we are compatible now and in the future.

Member

massie commented Mar 24, 2015

This is good stuff, Frank. We'll move our test environment on Jenkins over the Java 8 in order to make sure we are compatible now and in the future.

massie added a commit that referenced this pull request Mar 24, 2015

Merge pull request #619 from fnothaft/htsjdk-release
[ADAM-540] Move to new HTSJDK release; should support Java 8.

@massie massie merged commit 23ffce0 into bigdatagenomics:master Mar 24, 2015

1 check passed

default Merged build finished.
Details
@mylons

This comment has been minimized.

Show comment
Hide comment
@mylons

mylons Mar 24, 2015

woot! -- i'll pull and test.

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] ADAM ............................................... SUCCESS [  5.004 s]
[INFO] ADAM: Core ......................................... SUCCESS [01:13 min]
[INFO] ADAM: APIs for Java ................................ SUCCESS [ 12.027 s]
[INFO] ADAM: CLI .......................................... SUCCESS [ 27.850 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:58 min
[INFO] Finished at: 2015-03-24T10:26:40-07:00
[INFO] Final Memory: 45M/454M
[INFO] ------------------------------------------------------------------------

Well done!

mylons commented Mar 24, 2015

woot! -- i'll pull and test.

[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
[INFO] ADAM ............................................... SUCCESS [  5.004 s]
[INFO] ADAM: Core ......................................... SUCCESS [01:13 min]
[INFO] ADAM: APIs for Java ................................ SUCCESS [ 12.027 s]
[INFO] ADAM: CLI .......................................... SUCCESS [ 27.850 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:58 min
[INFO] Finished at: 2015-03-24T10:26:40-07:00
[INFO] Final Memory: 45M/454M
[INFO] ------------------------------------------------------------------------

Well done!

@fnothaft fnothaft deleted the fnothaft:htsjdk-release branch Mar 26, 2015

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment