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Published September 10, 2022 | Version v0.7.0
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apetkau/genomics-data-index: 0.7.0

Creators

  • 1. Public Health Agency of Canada, University of Manitoba

Description

  • [installation]: Downgraded scipy (scipy<1.9) in order to handle (https://github.com/biocore/scikit-bio/issues/1818) for installation of scikit-bio
  • [installation]: Fix sourmash to be sourmash<4.4 due to issues with sourmash search poducing empty CSV files in some cases.
  • [installation]: Fixed bcftools==1.13 and htslib==1.13 so that appropriate command-line parameters (filling tags with -t TYPE) work. This restriction could later be removed.
  • [analysis]: Fixed up order of conda channels for Snakemake pipeline dependencies (was causing installation issues).
  • [analysis]: Fixed bug with ambiguous character (N) in indel and adjusted iqtree parameters to just use the maximum specified threads instead of measuring optimal threads.

Files

apetkau/genomics-data-index-v0.7.0.zip

Files (2.6 MB)

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md5:33879417767d26dda5eb63534e1a9f99
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Additional details

Related works

Is supplement to
https://github.com/apetkau/genomics-data-index/tree/v0.7.0 (URL)