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- 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 <zoe.ma@curii.com>
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 <zoe.ma@curii.com>
- 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)
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Updated the WGS tutorial to make it run with the current base Docker image from which the containers can be built.