Update master to dev (release 2.5.0)#209

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Commits on Oct 14, 2016

Use config.groovy.template everywhere
Michael Milton (University of Melbourne)
committed
Don't use noverify by default
Michael Milton (University of Melbourne)
committed
Add java script to override default java
multimeric
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Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric
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Export JAVA_OPTS to everything
Michael Milton (University of Melbourne)
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Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric
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Move java script to bin
multimeric
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Stop java infinite loop
Michael Milton (University of Melbourne)
committed
Fix java version checks
Michael Milton (University of Melbourne)
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Commits on Oct 17, 2016

quoted java wrapper
supernifty
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Merge 2.3 changes
multimeric
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Commits on Oct 19, 2016

Commits on Oct 20, 2016

don't override batch parameter with default
supernifty
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Commits on Oct 22, 2016

Bpipe config branch PR (#188)
multimeric
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Commits on Oct 23, 2016

Basic rewrite of install process to use tools/install subdir
multimeric
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Commits on Oct 25, 2016

Finished rewrite; add various c libs to nectar
multimeric
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Installer fixes
multimeric
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Uploaded more assets
multimeric
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Installer fixes
multimeric
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Update current.manifest properly
multimeric
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Stop using c_libs
multimeric
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Fixed refence file nectar tasks
multimeric
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More data asset fixes
multimeric
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Made to_temp download tasks
multimeric
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More Fixes
Michael Milton (University of Melbourne)
committed
Fixed junit lib
multimeric
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Move copy from temp files
multimeric
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Fixed chromosome sizes task
multimeric
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Set uptodate for all install tasks
multimeric
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Merri fixes
Michael Milton (University of Melbourne)
committed
Merge branch 'install-rewrite' of https://github.com/MelbourneGenomics/cpipe into install-rewrite
Michael Milton (University of Melbourne)
committed

Commits on Oct 26, 2016

Fix copy_config tasks
multimeric
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Fix fastqc install
multimeric
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Merge branch 'install-rewrite' of github.com:MelbourneGenomics/cpipe into install-rewrite
multimeric
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Remove current manifest forever
multimeric
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Fix junit
multimeric
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Fixed ucsc nectar task
multimeric
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Fix for copying single files, fix overriding symlinks
multimeric
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Groovy-ngs fixes
Michael Milton (University of Melbourne)
committed
Installer working!
Michael Milton (University of Melbourne)
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Made all download tasks setup tasks, fixing the reinstallation issue
Michael Milton (University of Melbourne)
committed
Fixed data files not downloading correctly
Michael Milton (University of Melbourne)
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Fixed config groovy for nnew setup
Michael Milton (University of Melbourne)
committed
Re-added java emulator
Michael Milton (University of Melbourne)
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Added execute to java emulator
Michael Milton (University of Melbourne)
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More config groovy fixes
Michael Milton (University of Melbourne)
committed

Commits on Oct 27, 2016

Fixed dbsnp index
Michael Milton (University of Melbourne)
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Removed noverify default
Michael Milton (University of Melbourne)
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Commits on Oct 28, 2016

Add swift credentials to readme, export TMPDIR
multimeric
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Commits on Nov 1, 2016

Commits on Nov 2, 2016

Commits on Nov 4, 2016

Fix reported number of samples being reported as 1 less than reality
multimeric
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Commits on Nov 7, 2016

Commits on Nov 10, 2016

updated bpipe.config with more realistic walltimes
supernifty
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Commits on Nov 14, 2016

warn and continue if a sample has additional columns in qc_report CPIPE-199
supernifty
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Commits on Nov 18, 2016

Merge pull request #194 from MelbourneGenomics/metadata-parsing-qc
supernifty
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Commits on Nov 20, 2016

Commits on Nov 28, 2016

Commits on Nov 29, 2016

Finished basic manage batch implementation
multimeric
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Commits on Nov 30, 2016

Commits on Dec 1, 2016

Update errors in 2.4 docs
multimeric
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Commits on Dec 8, 2016

Commits on Dec 14, 2016

Commits on Jan 5, 2017

Finished validation using pandas_schema, editing using visidata
multimeric
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Commits on Jan 6, 2017

Python 3.6, Batch class improvements, manage batch work
multimeric
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Commits on Jan 9, 2017

Commits on Jan 11, 2017

Pipeline ID task
multimeric
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Commits on Jan 12, 2017

Commits on Jan 16, 2017

Rework python package, binary symlinks
multimeric
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Commits on Feb 3, 2017

Use entry_points instead of scripts, rewrite cpipe run script in python
multimeric
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Commits on Mar 17, 2017

Convert ./cpipe to python
multimeric
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Commits on Mar 21, 2017

Commits on Mar 22, 2017

Commits on Apr 4, 2017

Unit tests working
Ubuntu
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Use our ngs-utils
multimeric
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Commits on Apr 6, 2017

Update manual download tasks; make build.gradle for java libs
Ubuntu
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Commits on Apr 10, 2017

Use gradle for java libs, don't install them individually
Ubuntu
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Commits on Apr 20, 2017

Fixes for manual install; add cpipe bpipe command
Ubuntu
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Commits on Apr 21, 2017

Fix dependency clashes for gradle
Ubuntu
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Fix infinite java loop (CPIPE-215)
Ubuntu
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Move non-python scripts back to root directory
Ubuntu
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Add basic development docs
Ubuntu
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Update development.md
multimeric
authored

Commits on Apr 24, 2017

Commits on May 4, 2017

Index vep cache
Ubuntu
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Add upload_assets script to main cpipe repo
Ubuntu
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Update nectar assets
Ubuntu
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Environment file now starts new shell
Ubuntu
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Commits on May 5, 2017

Update vep_plugins
Ubuntu
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Installer fixed
Ubuntu
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Merge branch 'python-package' of https://github.com/MelbourneGenomics/cpipe into python-package
Ubuntu
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Added container to vep_plugins
Ubuntu
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Commits on May 8, 2017

More installer fixes
Ubuntu
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Commits on May 9, 2017

More installer fixes
Ubuntu
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Prompt user for queuing system
Ubuntu
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Commits on May 10, 2017

Fixed java lib installation
Michael Milton
committed
Merge branch 'python-package' of https://github.com/MelbourneGenomics/cpipe into python-package
Michael Milton
committed

Commits on May 11, 2017

Fixed java check
Michael Milton (University of Melbourne)
committed
Remove sample database update
Michael Milton (University of Melbourne)
committed
Fixed bpipe config template for torque
Michael Milton
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Merge branch 'python-package' of https://github.com/MelbourneGenomics/cpipe into python-package
Michael Milton
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Separated bpipe config generator into separate script; improved it
Michael Milton (University of Melbourne)
committed

Commits on May 30, 2017

Fix VCFAnno install; fix bpipe_config creator script
Michael Milton (University of Melbourne)
committed
Fixed batch sex validation; Started 2.5 documentation
multimeric
committed

Commits on Jun 1, 2017

Improved java check
Michael Milton (University of Melbourne)
committed
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into dev
Michael Milton (University of Melbourne)
committed
Update batch docs
multimeric
committed
Documentation updates, CLI fixes
multimeric
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Update document tables of contents
multimeric
committed

Commits on Jun 5, 2017

Documentation updates
Michael Milton (University of Melbourne)
committed
Update README.md
multimeric
authored
Update commands.md
multimeric
authored
Added md5 validation, improved batch create command, updated docs
Michael Milton (University of Melbourne)
committed
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into dev
Michael Milton (University of Melbourne)
committed
Re-added Visidata documentation
Michael Milton (University of Melbourne)
committed
Update commands.md
multimeric
authored

Commits on Jun 13, 2017

Updated vep plugin commit
Michael Milton (University of Melbourne)
committed

Commits on Jun 15, 2017

Fixed Grantham VEP plugin
Michael Milton (University of Melbourne)
committed
Attemped fix for md5 sum
Michael Milton (University of Melbourne)
committed
Permission error docs
Michael Milton (University of Melbourne)
committed
Add cpipe stop command
Michael Milton (University of Melbourne)
committed
Update bpipe to 0.9.9.4
Michael Milton (University of Melbourne)
committed
Update troubleshooting.md
multimeric
authored
Updated development docs
Michael Milton (University of Melbourne)
committed
Update index.md
multimeric
authored
Rename environment to 'cpipe'
Ubuntu
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Fix cpipe script
multimeric
committed
Update -NOVERIFY flag documentation
Michael Milton (University of Melbourne)
committed
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into dev
Michael Milton (University of Melbourne)
committed

Commits on Jun 16, 2017

Fix cpipe test
Michael Milton (University of Melbourne)
committed
Fix CLI scripts
Michael Milton (University of Melbourne)
committed

Commits on Jun 19, 2017

Document ./cpipe command rather than ./environment.sh
Michael Milton (University of Melbourne)
committed
Improved Docker docs
Michael Milton (University of Melbourne)
committed
Update docker.md
multimeric
authored
Update docker.md
multimeric
authored

Commits on Jun 20, 2017

Update README.md
multimeric
authored
Update README.md
multimeric
authored
Fixed installer help
Michael Milton (University of Melbourne)
committed
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into dev
Michael Milton (University of Melbourne)
committed
Update install.md
multimeric
authored
Update install.md
multimeric
authored

Commits on Jun 27, 2017

Fixed install.md TOC
Michael Milton (University of Melbourne)
committed
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into dev
Michael Milton (University of Melbourne)
committed

Commits on Jul 17, 2017

Lock down pip package versions
Ubuntu
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Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into HEAD
Ubuntu
committed

Commits on Jul 18, 2017

Update docker.md
multimeric
authored

Commits on Jan 12, 2018

Commits on Jan 20, 2018

Merge pull request #215 from aalborguh/pr
multimeric
authored