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Commits on Jun 9, 2017

• Install: ensure conda-forge in conda channels

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Commits on May 29, 2017

• Install: avoid certificate issues on AWS downloads

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Commits on May 20, 2017

• Avoid checking Miniconda certificate. Fixes #845

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Commits on Feb 16, 2017

• Update Miniconda download with changed URL

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Commits on Jan 26, 2017

• Include cyvcf2 when running GEMINI upgrade Fixes #808

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Commits on Feb 18, 2016

• Merge pull request #675 from bgruening/patch-2

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Commits on Feb 9, 2016

• Fix checking for permission to write config #662

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Commits on Feb 3, 2016

• Check for permissions before writing configuration file. Fixes #662

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Commits on Dec 29, 2015

• Up to date version of IPython with gemini 0.18.0 #478

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• Enable versioned installs for Galaxy support #478

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Commits on Dec 9, 2015

• Move to a single annotation-dir argument. Fix #633

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Commits on Dec 8, 2015

• Fix test suite message for dataonly update. Thanks to @schelhorn

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Commits on Dec 7, 2015

• More robust handling of git clone for tests

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Commits on Nov 30, 2015

• Merge pull request #617 from dakl/master

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Commits on Nov 13, 2015

• Tool and data directory arguments in original order

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• conda install: add gemini config if missing

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Commits on Nov 11, 2015

• Install script: back compatibility with older GEMINI data directories

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• Initial script for installing from conda only

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Commits on Nov 8, 2015

• New conda-only update process for GEMINI

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Commits on Oct 30, 2015

• Install script: get latest miniconda version

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Commits on Oct 28, 2015

• Add conda package installs for cyordereddict

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Commits on Oct 16, 2015

• Simplify installation of external tools

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Commits on Oct 11, 2015

• bcolz dependency: require fixed version of 0.11.x

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Commits on Sep 15, 2015

• Fix distributed loading of VEP with extra columns

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Commits on Aug 23, 2015

• Update to IPython 4.0

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• Additional handling of inputs missing ALT alleles

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Commits on Aug 22, 2015

• Handle no alts in allele-based annotation loading

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Commits on Aug 20, 2015

• Avoid use of tempdir for chunks when using IPython

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Commits on Aug 13, 2015

• Better SQLite debugging errors

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Commits on Jul 26, 2015

• Use pre-build pybedtools packages to avoid compile errors. Thanks to Julien Delafontaine and @brentp.

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Commits on Jul 21, 2015

• Avoid pulling in ipython 4.0 development branch. Thanks to Elizabeth Young

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Commits on Jul 13, 2015

• Avoid index error building query when 0 variants pass filters for insertion.

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Commits on Jul 12, 2015

• Only install grabix as a third party tool, requiring users to pre-install bedtools (for windower) and tabix (for annotate). Avoids issues with outdated installs conflicting with existing system pac…

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Commits on Jun 30, 2015

• Ensure extra files also make use of specified argument temporary directory, so all intermediates are in the same location. Fixes chapmanb/bcbio-nextgen#910 and can also help with consistent behavio…

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Commits on May 26, 2015

• Re-add previous fix that got removed: Catch issues where phred_likelihoods are not correctly specified in VCF as a list

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