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Merge main into dev#224

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evanroyrees merged 23 commits intodevKwanLab/Autometa:devfrom merge-mainKwanLab/Autometa:merge-mainCopy head branch name to clipboardJan 24, 2022

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Commits on Mar 15, 2020

• resolved #27 removed the 2.7 from the shebang of all the python scripts in the pipeline directory

  Sidduppal

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Commits on Mar 16, 2020

• Merge pull request #28 from Sidduppal/master

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Commits on Mar 26, 2020

• Updated Readme.md

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  jason-c-kwan

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Commits on Apr 2, 2020

• issue with nr.dmnd.md5 checking when this will never be written, resulting in always downloading nr.gz.Fixed file path handling to be less arch specific and updated variables for readability. (#35)

  evanroyrees

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Commits on Apr 7, 2020

• Added missing merged.dmp in database checking when using default autometa databases directory (#37)

  evanroyrees

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Commits on Apr 21, 2020

• Update issue templates

  evanroyrees

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• 📝 Add contribution guidelines, codeowners and PR templates. (#51)

  evanroyrees

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Commits on Jun 16, 2020

• Change the URLs to github from bitbucket (#89)

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  hyphaltip

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• 🐛 Fix taxid parsing bug. (#94)

  evanroyrees

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Commits on Jun 24, 2020

• Add files via upload

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  evanroyrees

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• Update support request

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Commits on Jul 28, 2020

• 🐛 handle case where all contigs are clustered in first DBSCAN round. (#105)

  evanroyrees

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Commits on Sep 3, 2020

• Dockerfile path bugfix (#107)

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  evanroyrees

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Commits on Nov 9, 2020

• Add link to (Automappa) interactive interface tool

  evanroyrees

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Commits on Nov 10, 2020

• Change User checklist python version from 3 to 2.7

  evanroyrees

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Commits on Feb 17, 2021

• Add support for keeping outdated databases (updating requires explicitly using --update flag) (#116)

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• Fix typo on line 186 in cluster_process.py ("completness" -> "completeness")

  ajlail98

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Commits on Feb 19, 2021

• Merge pull request #117 from ajlail98/cluster_process_bug

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Commits on Mar 12, 2021

• 📝 Update bug report template (master branch) (#131)

  evanroyrees

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Commits on Apr 14, 2021

• only try to generate hmm indexes if they do not exist, supporting global install with read-only access to marker folder (#139)

  hyphaltip

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Commits on Sep 13, 2021

• Upgrade to py3: version 1.0 deprecation of py2.7 (#180)

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  evanroyrees

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Commits on Dec 3, 2021

• Update README.md

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  evanroyrees

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Commits on Jan 24, 2022

• merge main into dev

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