Code

Update installation#363

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sebastian-luna-valero merged 48 commits intomasterCGATOxford/CGATPipelines:masterfrom SLV-update-installCGATOxford/CGATPipelines:SLV-update-installCopy head branch name to clipboardNov 8, 2017

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Commits

Commits on Jul 25, 2017

• include conda env export command

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Commits on Jul 28, 2017

• added conda env file and updated install script accordingly

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Commits on Aug 2, 2017

• improved env file for nosetests

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• improved install script

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• improved scripts to detect python and R deps

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Commits on Aug 3, 2017

• make --zip the default installation option

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• unified script to find Python and R deps

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Commits on Aug 4, 2017

• make cgat_check_deps.py self-contained and Py3-only

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• check python version in scripts/cgat_check_deps.py

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• pep8

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• add code to check 3rd party dependencies

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Commits on Sep 1, 2017

• before holiday commit

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Commits on Sep 15, 2017

• update cgat_conda_deps.sh and create conda env files for production pipelines

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• added conda env file for extra deps

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• updated install script

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Commits on Sep 22, 2017

• merge with latest master

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Commits on Sep 25, 2017

• add additional info to bash trap

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• pin deps versions; install bx-python properly

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Commits on Sep 28, 2017

• update MISC_DEPS in cgat_conda_deps.sh

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• add aux script to combine all conda deps from env files

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• exclude zinba from grep

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Commits on Sep 29, 2017

• add comment to output regarding creation; remove pydeps, rdeps, misc deps

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• output warnings for Py2 packages

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Commits on Oct 3, 2017

• rename conda env files to be consistent with jenkins testing

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Commits on Oct 4, 2017

• rename install options and update README.rst

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Commits on Oct 23, 2017

• add star as dependency to the extra conda env

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Commits on Oct 25, 2017

• fix conda and bx-python version

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• unknown input option for install script

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Commits on Oct 27, 2017

• parse bash statements with bashlex

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Commits on Oct 30, 2017

• exclude cgat_check_deps.py from test_import.py

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• pep8

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• clean up parameter interpolation properly

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• updated scripts to find deps

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• added new condition to get the string of statement.append

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Commits on Oct 31, 2017

• pep8

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Commits on Nov 1, 2017

• update conda environments

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• update conda environments

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• remove pip install bx-python from scripts/merge_conda_deps.sh

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• bugfix in finding deps recursively

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• added conda environment for production pipelines

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• Merge branch 'master' into SLV-update-install

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Commits on Nov 2, 2017

• enabled --production option for installation

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• Merge branch 'SLV-update-install' of github.com:CGATOxford/CGATPipelines into SLV-update-install

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• quiet conda installation

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• merge with latest master

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• add IDR

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• update conda environments with IDR

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Commits on Nov 7, 2017

• update conda envs

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