Remove credentials from ADAM pipeline #116
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Remove |
…otype prior to VQSR, and will recalculate some missing annotations.
So I've validated the credential removal part, but I'm running into a new fascinating bug (w00t!) that I haven't been able to root cause yet. Essentially, the BAM written out from ADAM and uploaded to S3 is corrupt. I'm modifying the scripts right now so that I can keep HDFS up after the ADAM pipeline completes so that I can root cause whether the issue is in ADAM's output or in the upload to S3. I'll report back as I know more. |
|
Actually, @hannes-ucsc, this is good to go WRT #107. I'll remove the |
hannes-ucsc
added a commit
that referenced
this pull request
Feb 25, 2016
Remove credentials from ADAM pipeline
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Resolves #107. First two commits are validated. I ran into an error during VQSR, which I believe c9abdf2 should fix, so I'm validating that now. Should have results by morning.