Commits

Breadcrumbs

History for

onsv

User selector

All users

All time

Commit history

Commits on Aug 23, 2014

• change versioned_installations path to Aarons repository

  bgruening

  committed
  2d998e8View commit details

  Copy full SHA for 2d998e8

  View code at this pointBrowse repository at this point

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.

  bgruening

  committed
  e110f0dView commit details

  Copy full SHA for e110f0d

  View code at this pointBrowse repository at this point

• remove unnecessary numpy installation call

  bgruening

  committed
  0a21359View commit details

  Copy full SHA for 0a21359

  View code at this pointBrowse repository at this point

• Install cloudbiolinux only if we want to install tools.

  bgruening

  committed
  f1d5215View commit details

  Copy full SHA for f1d5215

  View code at this pointBrowse repository at this point

Commits on Jul 18, 2014

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

  chapmanb

  committed
  49c30deView commit details

  Copy full SHA for 49c30de

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  c6c5fd6View commit details

  Copy full SHA for c6c5fd6

  View code at this pointBrowse repository at this point

Commits on May 19, 2014

• edit msg during install

  

  udp3f

  committed
  3edd866View commit details

  Copy full SHA for 3edd866

  View code at this pointBrowse repository at this point

Commits on May 7, 2014

• msg for GERP/CADD at install

  

  udp3f

  committed
  695caa3View commit details

  Copy full SHA for 695caa3

  View code at this pointBrowse repository at this point

Commits on Apr 30, 2014

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

  chapmanb

  committed
  9869aa8View commit details

  Copy full SHA for 9869aa8

  View code at this pointBrowse repository at this point

Commits on Apr 8, 2014

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

  chapmanb

  committed
  cac3c3dView commit details

  Copy full SHA for cac3c3d

  View code at this pointBrowse repository at this point

Commits on Mar 28, 2014

• API tweak

  

  arq5x

  committed
  0248463View commit details

  Copy full SHA for 0248463

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  96ffa1bView commit details

  Copy full SHA for 96ffa1b

  View code at this pointBrowse repository at this point

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…

  Show description for 4617776
  chapmanb

  committed
  4617776View commit details

  Copy full SHA for 4617776

  View code at this pointBrowse repository at this point

Commits on Feb 11, 2014

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

  chapmanb

  committed
  28755a5View commit details

  Copy full SHA for 28755a5

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  2cebc3bView commit details

  Copy full SHA for 2cebc3b

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  c6ffc25View commit details

  Copy full SHA for c6ffc25

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  eb81722View commit details

  Copy full SHA for eb81722

  View code at this pointBrowse repository at this point

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.

  chapmanb

  committed
  bd1fb11View commit details

  Copy full SHA for bd1fb11

  View code at this pointBrowse repository at this point

Commits on Dec 12, 2013

• Use batch mode for miniconda installation to avoid license interrupts

  chapmanb

  committed
  19e2b74View commit details

  Copy full SHA for 19e2b74

  View code at this pointBrowse repository at this point

Commits on Dec 11, 2013

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

  chapmanb

  committed
  5aad476View commit details

  Copy full SHA for 5aad476

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  5bc8279View commit details

  Copy full SHA for 5bc8279

  View code at this pointBrowse repository at this point

Commits on Dec 2, 2013

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

  chapmanb

  committed
  841c776View commit details

  Copy full SHA for 841c776

  View code at this pointBrowse repository at this point

Commits on Nov 17, 2013

• Avoid conda installation of distribute, which is deprecated

  chapmanb

  committed
  11297ceView commit details

  Copy full SHA for 11297ce

  View code at this pointBrowse repository at this point

Commits on Nov 7, 2013

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

  chapmanb

  committed
  58a4927View commit details

  Copy full SHA for 58a4927

  View code at this pointBrowse repository at this point

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)

  chapmanb

  committed
  552b9cbView commit details

  Copy full SHA for 552b9cb

  View code at this pointBrowse repository at this point

Commits on Oct 30, 2013

• Update Miniconda installer to latest version.

  chapmanb

  committed
  a7403f4View commit details

  Copy full SHA for a7403f4

  View code at this pointBrowse repository at this point

Commits on Sep 19, 2013

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

  chapmanb

  committed
  b504d5aView commit details

  Copy full SHA for b504d5a

  View code at this pointBrowse repository at this point

Commits on Sep 18, 2013

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

  chapmanb

  committed
  1e1e10aView commit details

  Copy full SHA for 1e1e10a

  View code at this pointBrowse repository at this point

Commits on Sep 10, 2013

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

  chapmanb

  committed
  089239fView commit details

  Copy full SHA for 089239f

  View code at this pointBrowse repository at this point

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

  committed
  a869133View commit details

  Copy full SHA for a869133

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  cd00824View commit details

  Copy full SHA for cd00824

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  160d40aView commit details

  Copy full SHA for 160d40a

  View code at this pointBrowse repository at this point

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

  chapmanb

  committed
  41389d4View commit details

  Copy full SHA for 41389d4

  View code at this pointBrowse repository at this point

Commits on Aug 26, 2013

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

  chapmanb

  committed
  9142869View commit details

  Copy full SHA for 9142869

  View code at this pointBrowse repository at this point

Commits on Aug 23, 2013

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

  chapmanb

  committed
  ac8ae3bView commit details

  Copy full SHA for ac8ae3b

  View code at this pointBrowse repository at this point