WGS Processing tutorial updates #1
Open
Conversation
This file contains hidden or 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
- In both the bwa/samtools and the clinvar-report containers, update the package names to be installed by the 'apt-get' commands. - When building external packages from source, refer to the ldconfig command by full path, because under /usr/sbin it may not be under the root user's PATH. - Build bwa 07.7.18 instead of 07.7.17, as the latter could be affected by a bug that makes it fail to build from source (see lh3/bwa#267 and BWA 07.7.18 release notes). Arvados-DCO-1.1-Signed-off-by: Zoë Ma <[email protected]>
In more recent versions of Python, the 'unicode()' global builtin is no longer there. In addition the binary IO for generating report doesn't appear necessary in our case anymore. Arvados-DCO-1.1-Signed-off-by: Zoë Ma <[email protected]>
- For bwa/samtools, update the executable path of 'bwa' to match the updated version 07.7.18 - For bwa/samtools, lower the number of CPU cores hinted from 16 to 6, because with the former it had trouble starting the job at all on systems with no more than 16 cores. - For generate-report, refer to the Python executable by the full path, because in the container built for that step, the bare 'python' command points to the Python instance installed by arvados-cwl-runner for which the Python libraries are not installed (the libraries are installed to the system Python directory)
zoe-translates
changed the title
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Outdated suggestions cannot be applied.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.
Updated the WGS tutorial to make it run with the current base Docker image from which the containers can be built.