travis conda debug #944
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travis conda debug #944
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…nstall openjdk at same time as solver
Add support for krakenuniq, kaiju to replace kraken and diamond in default pipelines. Both rely on customized krakenuniq/kaiju packages for custom functionality, like loading database from pipe or printing out all taxa hits (kaiju). Krona fixed to use hit counts as scores in report files directly, instead of counting the individual read classifications (which takes a long time).
This reverts commit a0ee882.
" With strict channel priority, packages in lower priority channels are not considered if a package with the same name appears in a higher priority channel." currently, the conda-forge is a higher-priority channel than defaults, however conda-forge has an older version of pigz than defaults
don't merge stderr with stdout since conda emits random messages to stderr that break json parsing when merged
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This hopefully includes changes to allow travis builds to resume, and incorporates KrakenUniq commits from @yesimon and an update to gap2seq update @notestaff. The commit history is noisy from all of the travis iteration, so this will need to be squashed/rebased before being merged.