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Python3 adaptation#291

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drkthomp wants to merge 53 commits intoBD2KGenomics:masterBD2KGenomics/protect:masterfrom drkthomp:python3-adaptationdrkthomp/protect:python3-adaptationCopy head branch name to clipboard

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Commits

Commits on Aug 23, 2020

• updated to python3

  

  dranion

  committed
  a5d062f

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• make develop runs

  

  dranion

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Commits on Aug 27, 2020

• add some of the extras, makes the install neater

  

  dranion

  committed
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• figuring out s3 references

  

  dranion

  committed
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• update to make it clear its python3

  

  dranion

  committed
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Commits on Sep 3, 2020

• mistake in ProTECT_config

  

  dranion

  committed
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Commits on Sep 5, 2020

• fixed to fastq files generated using picards SamToFastq

  drkthomp

  committed
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• fixing sort mechanism (TypeError: '<' not supported between instances of 'str' and 'int' was throwing due to str X,Y,M being sorted with 1...2)

  drkthomp

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• broke the makefile oops. actually installs ProTECT now.

  drkthomp

  committed
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• update universal options

  drkthomp

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Commits on Oct 8, 2020

• change to local

  drkthomp

  committed
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Commits on Oct 11, 2020

• final update, including mem changes

  drkthomp

  committed
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• error logs insufficient resources fixed 2020101023XX

  drkthomp

  committed
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• pip installing s3am is useless as it is python2. local only for now

  drkthomp

  committed
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• debug from 2 to 3 due to changes in check_output

  drkthomp

  committed
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• version is python2 only. TODO figure out fix

  drkthomp

  committed
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• ignore jobStore

  drkthomp

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• mem downgrade, not tested with toil (check still commented out)

  drkthomp

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• new error. possible /data path is wrong or docker?

  drkthomp

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Commits on Oct 19, 2020

• more exact error

  drkthomp

  committed
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Commits on Oct 20, 2020

• error

  drkthomp

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• file is not valid for python2. probably want iobase

  drkthomp

  committed
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Commits on Oct 23, 2020

• IOBASE import

  drkthomp

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Commits on Nov 8, 2020

• errors

  drkthomp

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Commits on Nov 23, 2020

• mustard errors

  

  Drew Thompson

  committed
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Commits on Nov 26, 2020

• core 80.0 error, hardcoding 20

  

  Drew Thompson

  committed
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• pandas ix deprication fix

  

  Drew Thompson

  committed
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Commits on Nov 28, 2020

• gunzip error

  

  Drew Thompson

  committed
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• gunzip error

  

  Drew Thompson

  committed
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• working run

  

  Drew Thompson

  committed
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• Update READ.me

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  drkthomp

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• record changes

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• Update README.md

  drkthomp

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• touchups

  drkthomp

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• Update README.md

  drkthomp

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• remove outdated bd2k-lib

  drkthomp

  committed
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• Merge branch 'master' of https://github.com/Dranion/protect

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  drkthomp

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• functioning virtualenv check

  drkthomp

  committed
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• ignore extras

  drkthomp

  committed
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• WIP: custom s3am and bd2k-lib py3 install

  drkthomp

  committed
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• Update MANUAL.md

  drkthomp

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• update manual to dranion ver

  drkthomp

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• quick push

  drkthomp

  committed
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• Merge branch 'master' of https://github.com/Dranion/protect

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  drkthomp

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• Delete \

  drkthomp

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• Update MANUAL.md

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  drkthomp

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• fix check_venv with toil fix

  drkthomp

  committed
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• Update MANUAL.md

  drkthomp

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Commits on Nov 29, 2020

• Update MANUAL.md

  drkthomp

  authored
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Commits on Dec 7, 2020

• debug statement cleanup

  drkthomp

  committed
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• remove extra

  drkthomp

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Commits on Jan 12, 2021

• Update README.md

  drkthomp

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• Remove custom yaml

  drkthomp

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