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Commits on Aug 23, 2014

• change versioned_installations path to Aarons repository

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Commits on Aug 22, 2014

• Add a new argument to specify a specific gemini version. This will fetch a pre-defined list of dependencies with hard version contraints.

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• remove unnecessary numpy installation call

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• Install cloudbiolinux only if we want to install tools.

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Commits on Jul 18, 2014

• Update installation to use new bcbio conda collection with pre-built bx-python packages. chapmanb/bcbio-nextgen#499

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Commits on Jun 13, 2014

• Include bcbio conda channel to provide up to date version of pysam (0.7.7) whih fixes a number of BAM parsing issues

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Commits on May 19, 2014

• edit msg during install

  

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Commits on May 7, 2014

• msg for GERP/CADD at install

  

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Commits on Apr 30, 2014

• Ensure that test repository matches installed gemini version when tagged on GitHub. Thanks to @udp3f

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Commits on Apr 8, 2014

• Do not use Miniconda-latest target for download until supported by OSX as well. Thanks to Jim Havrilla

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Commits on Mar 28, 2014

• API tweak

  

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Commits on Mar 27, 2014

• Small installation fixes: ensure we use latest Miniconda instead of bumping version and cleanup problem install issues immediately in case of partial install fail

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Commits on Feb 25, 2014

• Fix issue with missing __init__.py files that use namespace packages, which setuptools/pip toss away: update to latest ipython-cluster-helper with fix and manually patch for python-graph-core. Than…

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Commits on Feb 11, 2014

• Avoid issues with numpy 1.7/1.8 discrepency in automated conda installation. Fixes #264

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Commits on Jan 13, 2014

• More general fix for pip 1.5 compatibility, enabling install of python-graph-core and python-graph-dot from external non pypi sources

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• Allow retrieval of non-pypi dependency downloads with pip. Enables installation of python-graph-core in recent pip versions

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Commits on Jan 3, 2014

• Enable gemini installations with shared Anaconda directories. Allows gemini to play better with other gemini-like installer (bcbio-nextgen) and share Python dependencies

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Commits on Dec 25, 2013

• Provide ability to install gemini without data, and subsequently update only data. Allows separation of code from data to can distribute code-only versions in VMs and docker containers.

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Commits on Dec 12, 2013

• Use batch mode for miniconda installation to avoid license interrupts

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Commits on Dec 11, 2013

• Work around issue where pip fails on fixing distribute issues if distribute is already fine. chapmanb/bcbio-nextgen#207

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• Provide more flexible checking of curl dependency to avoid non-zero exist errors due to firewalls. chapmanb/bcbio-nextgen#207

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Commits on Dec 2, 2013

• Bump Miniconda installer to latest version. Thanks to Bertie Seyffert

  chapmanb

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Commits on Nov 17, 2013

• Avoid conda installation of distribute, which is deprecated

  chapmanb

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Commits on Nov 7, 2013

• Additional fixes to enable browser in standard installs: include jinja2 dependency and clean up requirements. Fixes #168

  chapmanb

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Commits on Nov 6, 2013

• Work around issue with broken concurrent versions of pip and easy_install where they ask for non-existant distribute versions (distribute==0.0)

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Commits on Oct 30, 2013

• Update Miniconda installer to latest version.

  chapmanb

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Commits on Sep 19, 2013

• Avoid using python environmental variables when running gemini, avoiding issues where PYTHONHOME or PYTHONPATH point to other library locations

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Commits on Sep 18, 2013

• Improve installation and update process to be resiliant to changes in local gemini repo that holds test scripts

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Commits on Sep 10, 2013

• Update gemini installer to use latest Miniconda release; remove extra install script in docs

  chapmanb

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Commits on Sep 3, 2013

• Giving up and removing sed fix for installer. It fixes a minor issue and causes too many unexpected problems

  chapmanb

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• Final installer fix for sed issues on MacOSX/Locales. Thanks to @jxchong

  chapmanb

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• Another attempt at cleaned up sed command to fix issues reported on MacOSX by @jxchong

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• Provide a cleaned up sed command to remove potential paging in Anaconda license. Thanks to @jxchong

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Commits on Aug 26, 2013

• Avoid pauses in Anaconda license that depend on screen size. Fixes chapmanb/cloudbiolinux#101

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Commits on Aug 23, 2013

• Detect partially prepared anaconda directories and recover by removing and re-installing. chapmanb/cloudbiolinux#105

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