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Running PR for Snakemakeification#164

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camillescott wants to merge 110 commits intomasterdib-lab/dammit:masterfrom decomposedib-lab/dammit:decomposeCopy head branch name to clipboard

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Commits

Commits on Nov 7, 2019

• add rename and stats components

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  e887d2a

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• add remap hmmer component

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• remove converted tasks

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• move busco parsers to fileio submodule

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• convert and filter components

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• Add conversion components

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• Get gff3 merge command working

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• add busco, transdecoder wrappers

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• ADd annotate component

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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• add rename-transcriptome wrapper

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Commits on Nov 8, 2019

• add transdecoder test data, rules

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• add busco rule, busco testdata

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• add last

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• add infernal wrapper and rule

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Commits on Nov 13, 2019

• First round of workflow structuring: database download

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• merge download rules

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Commits on Nov 15, 2019

• add transdecoder, last, infernal, hmmer wrappers

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Commits on Nov 16, 2019

• init hmmer, transdecoder workflows

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Commits on Dec 2, 2019

• code removal

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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Commits on Dec 10, 2019

• add yaml; init annot snakes

  bluegenes

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• init config changes; init main snake

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• yml db file

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Commits on Dec 12, 2019

• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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Commits on Dec 15, 2019

• working snakemake calls

  bluegenes

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• fix md5 downloads

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• ignore metalink for now

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Commits on Dec 16, 2019

• fix lastdb wrapper

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  faa5671

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• working transdecoder

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• getting... closer...

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• init env

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Commits on Feb 27, 2020

• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

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• upd busco env and wrapper

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Commits on Feb 28, 2020

• Remove cruft; use paths relative to installation dir for config and workflows; add workflows and configs to MANIFEST

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• Merge branch 'decompose' of github.com:camillescott/dammit into decompose

  camillescott

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• Get annotate working with install-relative paths and fix some formatting in annotate workflow

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Commits on Apr 17, 2020

• Update requirements

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• init setup snakefile

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• Remove sphinx

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• Remove _build folder

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• add mkdocs to dev reqs

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• Merge pull request #171 from dib-lab/update_reqs

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Commits on Apr 18, 2020

• init file conversion rules

  bluegenes

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• add gff3 file targets; fix rename txome wrapper

  bluegenes

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• Merge pull request #175 from dib-lab/add_conversion_rules

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Commits on Apr 23, 2020

• init shmlast wrapper, init shmlast and busco-v4 rules

  bluegenes

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Commits on Apr 24, 2020

• Refactor config and add config components

  camillescott

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• First pass unifying argparse and click interfaces

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• Add database dir as envvar

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• add .snakemake to gitignore

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• vendor cloup

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• Reorganize components into cloup groups

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• Remove busco tasks

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• remove tasks suybmodules

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  0c3f2d8

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• Fix regression in remap hmmer

  camillescott

  committed
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• add user db targets; init write config

  bluegenes

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  de2bd9e

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• Nuke the rest of dammit.tasks

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• Strip out more doit utils

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• add .vscode to gitignore

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• Add --version switch

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• Remove help from remap hmmer

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• enable print config

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Commits on Apr 25, 2020

• fix configfile printing

  bluegenes

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  86e545c

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• get dammit databases subcommand working again

  camillescott

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• change cmd order

  bluegenes

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• fix configfiles

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Commits on Apr 26, 2020

• add shmlast to pipeline yml; fix targeting

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Commits on Apr 27, 2020

• enable busco

  bluegenes

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• upd snkmk

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Commits on May 8, 2020

• refactor databases target gen

  camillescott

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• Bring in busco support

  camillescott

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• change busco wrapper to enable config

  bluegenes

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Commits on May 9, 2020

• comment out in progress rule

  bluegenes

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• Fix generate_annotation_targets, convert annotate to click parsing

  camillescott

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• merge in remove_argparse branch

  bluegenes

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  cded805

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• upd busco databases, fix busco targeting in run

  bluegenes

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  f1a2fe6

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• fix busco db in run

  bluegenes

  committed
  7af8112

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• working databases download

  bluegenes

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• working busco run!

  bluegenes

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• move addl setup rule to new branch

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Commits on May 15, 2020

• Merge pull request #179 from dib-lab/add_busco_config

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• Merge pull request #177 from dib-lab/remove_argparse

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• Add in best-hits step and fix database attribute in gff3 outputs

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Commits on May 16, 2020

• seems to be working

  bluegenes

  committed
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Commits on May 29, 2020

• Fix file output naming conventions, start migrating config locations

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Commits on May 30, 2020

• fix paths in ini config

  bluegenes

  committed
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• Rewire temp folders and add config output subcommands

  camillescott

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• Merge in BUSCO config fixes

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• Add temp directory cleaning command

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• Merge pull request #185 from dib-lab/extricate_fileio

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• add busco plotting

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• Merge branch 'decompose' into plot_busco

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Commits on Jun 26, 2020

• message formatting

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• Merge pull request #186 from dib-lab/plot_busco

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Commits on Aug 7, 2020

• Add tests for wrappers and components (#188)

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• use mamba for conda installations (#193)

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Commits on Oct 26, 2020

• Nuke it from orbit: general clean-up and bugfixing (#196)

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Commits on Oct 30, 2020

• Refactor GFF3 conversion code to fix ID non-determinism with threading (#200)

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Commits on Jan 13, 2021

• Snakefile formatting and file hierarchy cleanup (#201)

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Commits on Jan 14, 2021

• Remove busci.ini download as part of databases pipeline.

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• --n-threads can be set by environment variable

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Commits on Jan 15, 2021

• Add nice output to run commands

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Commits on Jan 22, 2021

• Remove extraneous print

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• Add an environment variable DAMMIT_TESTING_TEMP_BASE_DIR to set a static location of conda environment during test sessions; tempdir_factory is used per-session if this variable is not defined

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• Merge pull request #204 from dib-lab/ui_improvements

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• Merge pull request #205 from dib-lab/conda_testing_configuration

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Commits on Jan 23, 2021

• Add dammit-transcriptome-stats to annotation workflow

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Commits on Jan 25, 2021

• Add transcriptome_stats task to all pipelines

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• add rich to environment requirements

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